Alignments for a candidate for putA in Sinorhizobium medicae WSM419

GapMind for catabolism of small carbon sources

Alignments for a candidate for putA in Sinorhizobium medicae WSM419

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate YP_001325787.1 Smed_0092 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase

Query= reanno::azobra:AZOBR_RS23695
         (1235 letters)



>NCBI__GCF_000017145.1:YP_001325787.1
          Length = 1233

 Score = 1620 bits (4194), Expect = 0.0
 Identities = 853/1227 (69%), Positives = 961/1227 (78%), Gaps = 9/1227 (0%)

Query: 10   AAPGEAAPFADFAPPIRPATELRAAITAAYRRPEPECLPFLFEQASLPPGVITAAAATAR 69
            AAP   APFADFAPP++P + LR AITAAYRRPE ECLP L E A+       AA+ TAR
Sbjct: 13   AAP---APFADFAPPVQPQSTLRQAITAAYRRPETECLPPLVEAATQSKETREAASRTAR 69

Query: 70   KLITALRAKPRGRGVEGLIHEYSLSSQEGMALMCLAEALLRIPDHATRDALIRDKIAGGD 129
            KLI ALR K  G GVEGL+ EYSLSSQEG+ALMCLAEALLRIPD ATRDALIRDKIA G+
Sbjct: 70   KLIEALRGKHSGSGVEGLVQEYSLSSQEGVALMCLAEALLRIPDTATRDALIRDKIADGN 129

Query: 130  WQAHLGKGGSMFVNAATWGLLITGKLTSAGGEQALSSALTRLIARGGEPLIRRGVDFAMR 189
            W++HLG   S+FVNAATWGL++TGKLTS   +++LS+ALTRLI+R GEP+IRRGVD AMR
Sbjct: 130  WKSHLGGSRSLFVNAATWGLVVTGKLTSTVNDRSLSAALTRLISRCGEPVIRRGVDMAMR 189

Query: 190  MMGEQFVTGQTIQEALTNARTMEAEGFRYSYDMLGEAALTAEDAARYYADYVNAIHAIGT 249
            MMGEQFVTG+TI+EAL  ++ +E +GFRYSYDMLGEAA TA DA RYY DY +AIHAIG 
Sbjct: 190  MMGEQFVTGETIEEALKRSKELEGKGFRYSYDMLGEAATTAADAERYYRDYESAIHAIGK 249

Query: 250  ASAGRGVYEGPGISIKLSAIHPRYSRAQADRVMDELLPRVKALALLAKGYDIGLNIDAEE 309
            ASAGRG+YEGPGISIKLSA+HPRY+RAQA RVM ELLP+VKALALLA+ YDIGLNIDAEE
Sbjct: 250  ASAGRGIYEGPGISIKLSALHPRYTRAQAVRVMGELLPKVKALALLARKYDIGLNIDAEE 309

Query: 310  ADRLELSLDLMESLCFDPDLAGWNGIGFVVQAYGKRCPYVIDFLIDLARRSGHRLMIRLV 369
            ADRLELSLDL+E LC D +L+GWNG+GFVVQAYGKRCP+V+DF+IDLARRSG R+M+RLV
Sbjct: 310  ADRLELSLDLLEELCLDAELSGWNGMGFVVQAYGKRCPFVLDFVIDLARRSGRRIMVRLV 369

Query: 370  KGAYWDSEIKRAQLDGLPDFPVYTRKVYTDVSYVACARKLLAAPEAVFPQFATHNAQTLA 429
            KGAYWD+EIKRAQLDGL DFPV+TRK++TDVSY+ACA KLLAA + +FPQFATHNAQTLA
Sbjct: 370  KGAYWDAEIKRAQLDGLEDFPVFTRKIHTDVSYLACAAKLLAATDVIFPQFATHNAQTLA 429

Query: 430  TIYEMAGSDFQVGKYEFQCLHGMGEPLYKEVV--GPLKRPCRIYAPVGTHETLLAYLVRR 487
             IY MAG DFQVGKYEFQCLHGMGEPLY+EVV  G L RPCRIYAPVGTHETLLAYLVRR
Sbjct: 430  AIYHMAGKDFQVGKYEFQCLHGMGEPLYEEVVGLGNLDRPCRIYAPVGTHETLLAYLVRR 489

Query: 488  LLENGANSSFVNRIADPAVPVDELVADPVAVARAIAPTGAPHALIALPRNLYAPERANSA 547
            LLENGANSSFV+RI DP V +DEL+ADPV + R +   GA H  IALP  L+   R NSA
Sbjct: 490  LLENGANSSFVHRINDPKVSIDELIADPVEIVRGMPVVGARHDKIALPAELFGDSRTNSA 549

Query: 548  GIDLSDETELARLSAALSASAEMTWTAAPLLADGERAGQAQPVRNPADRRDVVGSVTEAS 607
            G+DLS+E  LA L+ AL ASA   WT  P LA G  AG+  PV NP D RDVVGSVTE S
Sbjct: 550  GLDLSNEETLASLTDALKASAANGWTCVPRLATGPVAGETLPVLNPGDHRDVVGSVTETS 609

Query: 608  EALVAEAFGHAVAAASAWAATPPEERAASLFRAADTMQERMPTLLGLIVREAGKSLPNAI 667
            E     A   A  AA+ WAA  P ERAA L RAA  MQ RMPTLLGLI+REAGKS  NAI
Sbjct: 610  EEDARRAARLAAEAAADWAAVSPSERAACLDRAAGLMQARMPTLLGLIIREAGKSALNAI 669

Query: 668  AEVREAIDFLRYYGAQVRDRFDNATHRPLGPVVCISPWNFPLAIFSGQIAAALAAGNPVL 727
            AEVREAIDFLRYY  Q R R     HRPLGPVVCISPWNFPLAIF+GQIAAAL AGNPVL
Sbjct: 670  AEVREAIDFLRYYAEQTR-RTLGPGHRPLGPVVCISPWNFPLAIFTGQIAAALVAGNPVL 728

Query: 728  AKPAEETPLIAAEAVRILHAAGIPAGALQLLPGAGEVGAALVGHEAVRGVMFTGSTEVAR 787
            AKPAEETPLIAAE VRIL  AGIPA ALQLLPG G +GAALV      GVMFTGSTEVAR
Sbjct: 729  AKPAEETPLIAAEGVRILQEAGIPARALQLLPGDGRIGAALVAAPETAGVMFTGSTEVAR 788

Query: 788  LIQRQLAGRLLPDGAPIPLIAETGGQNAMIVDSSALAEQVVGDVIASAFDSAGQRCSALR 847
            LIQ QLA RL   G PIPLIAETGGQNAMIVDSSALAEQVVGDVIASAFDSAGQRCSALR
Sbjct: 789  LIQAQLADRLSLAGRPIPLIAETGGQNAMIVDSSALAEQVVGDVIASAFDSAGQRCSALR 848

Query: 848  ILCLQEDVADRTLAMLKGAMRELRIGNPDRLAVDVGPVISEEARATIAAHIEAMRAKGRN 907
            +LCLQEDVA+R L MLKGA+ EL+IG  DRL+VDVGPVI+ EA+  I  HI  MR  GR 
Sbjct: 849  VLCLQEDVAERILTMLKGALHELQIGRTDRLSVDVGPVITSEAKENIEKHIARMRELGRK 908

Query: 908  VEFLPLPAETADGTFIAPTVIEIGGIHELEREVFGPVLHVVRFHRDDLDALVDSINATGY 967
            VE + L +ET  GTF+ PT+IE+  + +LEREVFGPVLHV+R+ RD LD LVD INATGY
Sbjct: 909  VEQIGLASETDQGTFVPPTIIELEKLSDLEREVFGPVLHVIRYRRDGLDRLVDDINATGY 968

Query: 968  GLTFGLHTRIDATIERVTGRIGAGNVYVNRNTIGAVVGVQPFGGHGLSGTGPKAGGPLYL 1027
            GLTFGLHTR+D TI  VT RI AGN+Y+NRN IGAVVGVQPFGG GLSGTGPKAGGPLYL
Sbjct: 969  GLTFGLHTRLDETIAHVTSRIKAGNLYINRNIIGAVVGVQPFGGRGLSGTGPKAGGPLYL 1028

Query: 1028 SRLLSRRPKGWLEFRGPDAARAAGLAYGEWLRAKGFTAEASRCAGYVARSAIGGGAELNG 1087
             RL++  P                L + +WL  KG  AEA       + SA+G   EL G
Sbjct: 1029 GRLVATAPVP--PQHSSVHTDPVLLDFTKWLDGKGACAEAEAARNAGSSSALGLDLELPG 1086

Query: 1088 PVGERNLYELHGRGRVLLLPQTRTGLLLQLGAVLATGNSAAVDAPPDLAELLRGLPPALA 1147
            PVGERNLY LH RGR+LL+P T +GL  QL A LATGNS  +DA   L   L+ LP  + 
Sbjct: 1087 PVGERNLYTLHARGRILLVPATASGLYHQLAAALATGNSVVIDAASGLQPSLKDLPQTVG 1146

Query: 1148 ARVRTTADWRDVGPLAAVLVEGDRERVTAINRRVADLPGPILLVQAATAEALAAGRGEGY 1207
             RV  + DW   GP A  LVEGD ER+ A+N+ +A LPGP+LLVQAA++E +A    + Y
Sbjct: 1147 LRVSWSKDWAADGPFAGALVEGDGERIRAVNKAIAALPGPLLLVQAASSEEIAR-NPDAY 1205

Query: 1208 DLDLLLNERSVSVNTAAAGGNASLVAM 1234
             L+ L+ E S S+NTAAAGGNASL+A+
Sbjct: 1206 CLNWLVEEVSASINTAAAGGNASLMAI 1232


Lambda     K      H
   0.319    0.136    0.396 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 3769
Number of extensions: 166
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 1235
Length of database: 1233
Length adjustment: 48
Effective length of query: 1187
Effective length of database: 1185
Effective search space:  1406595
Effective search space used:  1406595
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 59 (27.3 bits)

Align candidate YP_001325787.1 Smed_0092 (bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase)
to HMM TIGR01238 (delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR01238.hmm
# target sequence database:        /tmp/gapView.4469.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01238  [M=500]
Accession:   TIGR01238
Description: D1pyr5carbox3: delta-1-pyrroline-5-carboxylate dehydrogenase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                 Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     4e-224  730.6   1.0   7.5e-224  729.7   0.1    1.7  2  lcl|NCBI__GCF_000017145.1:YP_001325787.1  Smed_0092 bifunctional proline d


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000017145.1:YP_001325787.1  Smed_0092 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydr
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  729.7   0.1  7.5e-224  7.5e-224       1     497 [.     539    1033 ..     539    1036 .. 0.98
   2 ?   -1.3   0.1      0.03      0.03     180     196 ..    1115    1131 ..    1110    1138 .. 0.84

  Alignments for each domain:
  == domain 1  score: 729.7 bits;  conditional E-value: 7.5e-224
                                 TIGR01238    1 dlygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdivGq 67  
                                                +l+g++r+ns+G+dl+ne++l+sl + l+++aa+ +  +p ++  ++  ge+ pv np d++d+vG 
  lcl|NCBI__GCF_000017145.1:YP_001325787.1  539 ELFGDSRTNSAGLDLSNEETLASLTDALKASAANGWTCVPRLATGPV-AGETLPVLNPGDHRDVVGS 604 
                                                79****************************************76666.58999************** PP

                                 TIGR01238   68 vseadaaevqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiae 134 
                                                v+e++++++++a   a +a+a w a+ + eraa+l+r+a l++ +mp+l++l++reaGk+  naiae
  lcl|NCBI__GCF_000017145.1:YP_001325787.1  605 VTETSEEDARRAARLAAEAAADWAAVSPSERAACLDRAAGLMQARMPTLLGLIIREAGKSALNAIAE 671 
                                                ******************************************************************* PP

                                 TIGR01238  135 vreavdflryyakqvedvldeesakalGavvcispwnfplaiftGqiaaalaaGntviakpaeqtsl 201 
                                                vrea+dflryya+q + +l+   +++lG+vvcispwnfplaiftGqiaaal+aGn v+akpae+t+l
  lcl|NCBI__GCF_000017145.1:YP_001325787.1  672 VREAIDFLRYYAEQTRRTLGPG-HRPLGPVVCISPWNFPLAIFTGQIAAALVAGNPVLAKPAEETPL 737 
                                                ********************98.******************************************** PP

                                 TIGR01238  202 iaaravellqeaGvpagviqllpGrGedvGaaltsderiaGviftGstevarlinkalakredap.. 266 
                                                iaa++v +lqeaG+pa ++qllpG G  +Gaal + +  aGv+ftGstevarli+ +la+r      
  lcl|NCBI__GCF_000017145.1:YP_001325787.1  738 IAAEGVRILQEAGIPARALQLLPGDGR-IGAALVAAPETAGVMFTGSTEVARLIQAQLADRLSLAgr 803 
                                                **************************9.*********************************875444 PP

                                 TIGR01238  267 .vpliaetGGqnamivdstalaeqvvadvlasafdsaGqrcsalrvlcvqedvadrvltlikGamde 332 
                                                 +pliaetGGqnamivds+alaeqvv dv+asafdsaGqrcsalrvlc+qedva+r+lt++kGa++e
  lcl|NCBI__GCF_000017145.1:YP_001325787.1  804 pIPLIAETGGQNAMIVDSSALAEQVVGDVIASAFDSAGQRCSALRVLCLQEDVAERILTMLKGALHE 870 
                                                4****************************************************************** PP

                                 TIGR01238  333 lkvgkpirlttdvGpvidaeakqnllahiekmkakakkvaqvkleddvesekgtfvaptlfelddld 399 
                                                l++g+  rl  dvGpvi +eak+n+++hi +m++ ++kv q+ l++  e+++gtfv+pt++el++l+
  lcl|NCBI__GCF_000017145.1:YP_001325787.1  871 LQIGRTDRLSVDVGPVITSEAKENIEKHIARMRELGRKVEQIGLAS--ETDQGTFVPPTIIELEKLS 935 
                                                ********************************************99..999**************** PP

                                 TIGR01238  400 elkkevfGpvlhvvrykadeldkvvdkinakGygltlGvhsrieetvrqiekrakvGnvyvnrnlvG 466 
                                                +l++evfGpvlhv+ry++d ld++vd ina+Gyglt+G+h+r +et++++++r+k+Gn+y+nrn++G
  lcl|NCBI__GCF_000017145.1:YP_001325787.1  936 DLEREVFGPVLHVIRYRRDGLDRLVDDINATGYGLTFGLHTRLDETIAHVTSRIKAGNLYINRNIIG 1002
                                                ******************************************************************* PP

                                 TIGR01238  467 avvGvqpfGGeGlsGtGpkaGGplylyrltr 497 
                                                avvGvqpfGG+GlsGtGpkaGGplyl rl+ 
  lcl|NCBI__GCF_000017145.1:YP_001325787.1 1003 AVVGVQPFGGRGLSGTGPKAGGPLYLGRLVA 1033
                                                ****************************986 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.03
                                 TIGR01238  180 qiaaalaaGntviakpa 196 
                                                q+aaala+Gn+v+   a
  lcl|NCBI__GCF_000017145.1:YP_001325787.1 1115 QLAAALATGNSVVIDAA 1131
                                                89**********98766 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (500 nodes)
Target sequences:                          1  (1233 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 22.35
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources