GapMind for catabolism of small carbon sources

 

Aligments for a candidate for putA in Sphingomonas koreensis DSMZ 15582

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate Ga0059261_3926 Ga0059261_3926 L-proline dehydrogenase (EC 1.5.99.8)/delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.5.1.12)

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



>lcl|FitnessBrowser__Korea:Ga0059261_3926 Ga0059261_3926 L-proline
            dehydrogenase (EC
            1.5.99.8)/delta-1-pyrroline-5-carboxylate dehydrogenase
            (EC 1.5.1.12)
          Length = 1199

 Score = 1573 bits (4072), Expect = 0.0
 Identities = 829/1224 (67%), Positives = 941/1224 (76%), Gaps = 31/1224 (2%)

Query: 16   APFADFAPPIRPATELRAAITAAYRRPEPECLPFLFEQASLPPGVITAAAATARKLITAL 75
            APFADFAPPIRP T LR+AITAAYRRPEPEC+P L EQASLP G   AA  TA  LITAL
Sbjct: 3    APFADFAPPIRPQTPLRSAITAAYRRPEPECVPPLVEQASLPEGTREAARITASTLITAL 62

Query: 76   RAKPRGRGVEGLIHEYSLSSQEGMALMCLAEALLRIPDHATRDALIRDKIAGGDWQAHLG 135
            RAK +G GVEGL+ EY+LSSQEG+ALMCLAEALLRIPD ATRDALIRDKIA GDW++H+G
Sbjct: 63   RAKHKGTGVEGLVQEYALSSQEGVALMCLAEALLRIPDDATRDALIRDKIADGDWKSHIG 122

Query: 136  KGGSMFVNAATWGLLITGKLTSAGGEQALSSALTRLIARGGEPLIRRGVDFAMRMMGEQF 195
             G S+FVNAATWGL++TGKLT +  +  L +ALTRLIAR GEP+IRRGVD AMRMMGEQF
Sbjct: 123  DGRSLFVNAATWGLVVTGKLTGSVNDAGLGAALTRLIARAGEPVIRRGVDMAMRMMGEQF 182

Query: 196  VTGQTIQEALTNARTMEAEGFRYSYDMLGEAALTAEDAARYYADYVNAIHAIGTASAGRG 255
            VTG+TI EAL  ART+EA GF+YSYDMLGEAA T  DA RYY DY NA+ AIG ASAGRG
Sbjct: 183  VTGETIAEALKRARTLEARGFQYSYDMLGEAATTMADADRYYRDYENAVRAIGEASAGRG 242

Query: 256  VYEGPGISIKLSAIHPRYSRAQADRVMDELLPRVKALALLAKGYDIGLNIDAEEADRLEL 315
            V  GPGISIKLSA+HPRY+RAQA RVMDELLP+VKALA+LA+GYDIG NIDAEEADRLEL
Sbjct: 243  VVGGPGISIKLSALHPRYARAQAGRVMDELLPKVKALAVLARGYDIGFNIDAEEADRLEL 302

Query: 316  SLDLMESLCFDPDLAGWNGIGFVVQAYGKRCPYVIDFLIDLARRSGHRLMIRLVKGAYWD 375
            SLDL+ESL  DPDL GW+G+GFVVQAYGKRCP+VID+++DLA+R+  R+M+RLVKGAYWD
Sbjct: 303  SLDLLESLALDPDLKGWDGLGFVVQAYGKRCPFVIDWIVDLAQRADRRIMVRLVKGAYWD 362

Query: 376  SEIKRAQLDGLPDFPVYTRKVYTDVSYVACARKLLAAPEAVFPQFATHNAQTLATIYEMA 435
            +EIKRAQ+DGLPDFPVYTRK+YTDV+Y+ACARKLLA  + +FPQFATHNAQTLATIY+MA
Sbjct: 363  AEIKRAQVDGLPDFPVYTRKIYTDVAYIACARKLLANRDRIFPQFATHNAQTLATIYQMA 422

Query: 436  GSDFQVGKYEFQCLHGMGEPLYKEVVG--PLKRPCRIYAPVGTHETLLAYLVRRLLENGA 493
            G DF VG YEFQCLHGMGEPLY EVVG   L RPCRIYAPVGTHETLLAYLVRRLLENGA
Sbjct: 423  GPDFSVGDYEFQCLHGMGEPLYDEVVGATKLNRPCRIYAPVGTHETLLAYLVRRLLENGA 482

Query: 494  NSSFVNRIADPAVPVDELVADPVAVARAIAPTGAPHALIALPRNLYAPERANSAGIDLSD 553
            NSSFVNRIADP V + ELVADPV   R++   GA H LIALP  LY   R NS G+DLS+
Sbjct: 483  NSSFVNRIADPEVSIAELVADPVDQVRSMDVVGAKHPLIALPTGLYGARR-NSEGLDLSN 541

Query: 554  ETELARLSAALSASAEMTWTAAPLLADGERAGQAQPVRNPADRRDVVGSVTEASEALVAE 613
            E  LA L+A+L  SA   W A P     +R G ++PV NPAD +DVVG+V E +      
Sbjct: 542  ENVLAELAASLKVSAAAGWAAEP----ADRIGTSRPVYNPADGKDVVGTVVEVTPEAAQT 597

Query: 614  AFGHAVAAASAWAATPPEERAASLFRAADTMQERMPTLLGLIVREAGKSLPNAIAEVREA 673
            A   A AAA+ WAA  P ERAA L RAAD MQ+RM  L+GLI+REAGKS PNAIAEVREA
Sbjct: 598  AVATAQAAAADWAAVAPAERAACLDRAADIMQDRMQILMGLIIREAGKSAPNAIAEVREA 657

Query: 674  IDFLRYYGAQVRDRFDNATHRPLGPVVCISPWNFPLAIFSGQIAAALAAGNPVLAKPAEE 733
            IDFLRYY  Q R     A H+PLG V CISPWNFPLAIF+GQ+AAAL AGN VLAKPAEE
Sbjct: 658  IDFLRYYAEQARAML-GAAHKPLGAVTCISPWNFPLAIFTGQVAAALVAGNTVLAKPAEE 716

Query: 734  TPLIAAEAVRILHAAGIPAGALQLLPGAGEVGAALVGHEAVRGVMFTGSTEVARLIQRQL 793
            TPLIAA+ V ILH AGIPA ALQL+PG G +GAALV     + VMFTGSTEVAR+IQ++L
Sbjct: 717  TPLIAAQGVSILHEAGIPAAALQLVPGDGRIGAALVAAPGTQAVMFTGSTEVARIIQKEL 776

Query: 794  AGRLLPDGAPIPLIAETGGQNAMIVDSSALAEQVVGDVIASAFDSAGQRCSALRILCLQE 853
            A RL   G P+P IAETGGQNAMIVDSSALAEQVVGDVIASAFDSAGQRCSALR+LCLQ+
Sbjct: 777  AKRLTDGGDPVPFIAETGGQNAMIVDSSALAEQVVGDVIASAFDSAGQRCSALRVLCLQD 836

Query: 854  DVADRTLAMLKGAMRELRIGNPDRLAVDVGPVISEEARATIAAHIEAMRAKGRNVEFLPL 913
            DVADR L MLKGA+ EL IG  D L+ D+GPVI+ EA+A I  HI  M   GR VE + L
Sbjct: 837  DVADRILVMLKGALHELSIGRTDSLSTDIGPVITAEAKANIEGHIARMLGMGRGVEQIEL 896

Query: 914  PAETADGTFIAPTVIEIGGIHELEREVFGPVLHVVRFHRDDLDALVDSINATGYGLTFGL 973
              ETA GTF+ PT+IE+  I +LEREVFGPVLHVVR+ R DLD ++D+INATGYGLTFGL
Sbjct: 897  AGETAQGTFVPPTIIELQSIADLEREVFGPVLHVVRYKRRDLDRVIDAINATGYGLTFGL 956

Query: 974  HTRIDATIERVTGRIGAGNVYVNRNTIGAVVGVQPFGGHGLSGTGPKAGGPLYLSRLLSR 1033
            HTR+D TI  V+ R+ AGN+Y+NRN IGAVVGVQPFGG GLSGTGPKAGGPLYL RL+  
Sbjct: 957  HTRLDETIAHVSQRVEAGNLYINRNIIGAVVGVQPFGGRGLSGTGPKAGGPLYLGRLVQT 1016

Query: 1034 R--PKGWLEFRGPDAARAAGLAYGEWLRAKGFTAEASRCAGYVARSAIGGGAELNGPVGE 1091
               P G        A R   L    WL  +G   EA+R AG    S +G   EL GPVGE
Sbjct: 1017 ATVPPGVASDTSDPALRDFAL----WLGEQG---EAARAAG--EASLLGAEVELPGPVGE 1067

Query: 1092 RNLYELHGRGRVLLLPQTRTGLLLQLGAVLATGNSAAVDAPPDLAELLRGLPPALAARVR 1151
            RN+Y LH RG VLLLP+TR GL+ Q+ A LATGN A +       E L GLP  +AAR+ 
Sbjct: 1068 RNIYALHPRGSVLLLPKTREGLIAQVSAALATGNRAVIGNTALRGE-LAGLPERVAARLS 1126

Query: 1152 TTADWRDVGPLAAVLVEGDRERVTAINRRVADLPGPILLVQAATAEALAAGRGEGYDLDL 1211
               DWR  GP    L+EGD    +A    +A LPGPI+L QA T             LD 
Sbjct: 1127 WADDWRKAGPYGGALIEGDAAARSAALAEIAALPGPIVLAQAGTPR-----------LDW 1175

Query: 1212 LLNERSVSVNTAAAGGNASLVAMS 1235
            L+ E S SVNT AAGGNASL+A++
Sbjct: 1176 LVEEVSTSVNTTAAGGNASLMAVA 1199


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: 3787
Number of extensions: 157
Number of successful extensions: 8
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: 1199
Length adjustment: 47
Effective length of query: 1188
Effective length of database: 1152
Effective search space:  1368576
Effective search space used:  1368576
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 Ga0059261_3926 Ga0059261_3926 (L-proline dehydrogenase (EC 1.5.99.8)/delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.5.1.12))
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.7298.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.7e-219  715.4   7.7   3.2e-219  714.5   7.7    1.4  1  lcl|FitnessBrowser__Korea:Ga0059261_3926  Ga0059261_3926 L-proline dehydro


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_3926  Ga0059261_3926 L-proline dehydrogenase (EC 1.5.99.8)/delta-1-pyrroline-5-ca
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  714.5   7.7  3.2e-219  3.2e-219       2     498 ..     527    1016 ..     526    1018 .. 0.98

  Alignments for each domain:
  == domain 1  score: 714.5 bits;  conditional E-value: 3.2e-219
                                 TIGR01238    2 lygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdivGqv 68  
                                                lyg  r+ns G+dl+ne++l++l ++l+ +aa  + a p         g  +pv npad kd+vG+v
  lcl|FitnessBrowser__Korea:Ga0059261_3926  527 LYGA-RRNSEGLDLSNENVLAELAASLKVSAAAGWAAEPA-----DRIGTSRPVYNPADGKDVVGTV 587 
                                                7888.******************************99885.....467999**************** PP

                                 TIGR01238   69 seadaaevqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiaev 135 
                                                 e   + +q av +a+aa+a w a+ ++eraa+l+r+ad+++ +m  l++l++reaGk+  naiaev
  lcl|FitnessBrowser__Korea:Ga0059261_3926  588 VEVTPEAAQTAVATAQAAAADWAAVAPAERAACLDRAADIMQDRMQILMGLIIREAGKSAPNAIAEV 654 
                                                ******************************************************************* PP

                                 TIGR01238  136 reavdflryyakqvedvldeesakalGavvcispwnfplaiftGqiaaalaaGntviakpaeqtsli 202 
                                                rea+dflryya+q++  l+   +k+lGav cispwnfplaiftGq+aaal+aGntv+akpae+t+li
  lcl|FitnessBrowser__Korea:Ga0059261_3926  655 REAIDFLRYYAEQARAMLGAA-HKPLGAVTCISPWNFPLAIFTGQVAAALVAGNTVLAKPAEETPLI 720 
                                                ***************999988.********************************************* PP

                                 TIGR01238  203 aaravellqeaGvpagviqllpGrGedvGaaltsderiaGviftGstevarlinkalakredap... 266 
                                                aa++v++l+eaG+pa+++ql+pG G  +Gaal + +  + v+ftGstevar i+k+lakr  +    
  lcl|FitnessBrowser__Korea:Ga0059261_3926  721 AAQGVSILHEAGIPAAALQLVPGDGR-IGAALVAAPGTQAVMFTGSTEVARIIQKELAKRLTDGgdp 786 
                                                *************************9.*********************************8753344 PP

                                 TIGR01238  267 vpliaetGGqnamivdstalaeqvvadvlasafdsaGqrcsalrvlcvqedvadrvltlikGamdel 333 
                                                vp+iaetGGqnamivds+alaeqvv dv+asafdsaGqrcsalrvlc+q+dvadr+l ++kGa++el
  lcl|FitnessBrowser__Korea:Ga0059261_3926  787 VPFIAETGGQNAMIVDSSALAEQVVGDVIASAFDSAGQRCSALRVLCLQDDVADRILVMLKGALHEL 853 
                                                ******************************************************************* PP

                                 TIGR01238  334 kvgkpirlttdvGpvidaeakqnllahiekmkakakkvaqvkleddvesekgtfvaptlfelddlde 400 
                                                 +g+   l td+Gpvi aeak n++ hi +m ++++ v q+ l+   e+ +gtfv+pt++el+++++
  lcl|FitnessBrowser__Korea:Ga0059261_3926  854 SIGRTDSLSTDIGPVITAEAKANIEGHIARMLGMGRGVEQIELAG--ETAQGTFVPPTIIELQSIAD 918 
                                                *******************************************99..999***************** PP

                                 TIGR01238  401 lkkevfGpvlhvvrykadeldkvvdkinakGygltlGvhsrieetvrqiekrakvGnvyvnrnlvGa 467 
                                                l++evfGpvlhvvryk+++ld+v+d ina+Gyglt+G+h+r +et++++ +r+++Gn+y+nrn++Ga
  lcl|FitnessBrowser__Korea:Ga0059261_3926  919 LEREVFGPVLHVVRYKRRDLDRVIDAINATGYGLTFGLHTRLDETIAHVSQRVEAGNLYINRNIIGA 985 
                                                ******************************************************************* PP

                                 TIGR01238  468 vvGvqpfGGeGlsGtGpkaGGplylyrltrv 498 
                                                vvGvqpfGG+GlsGtGpkaGGplyl rl+++
  lcl|FitnessBrowser__Korea:Ga0059261_3926  986 VVGVQPFGGRGLSGTGPKAGGPLYLGRLVQT 1016
                                                ****************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (500 nodes)
Target sequences:                          1  (1199 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: 00:00:00.03
# Mc/sec: 19.64
//
[ok]

This GapMind analysis is from Sep 17 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:

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:

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:

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 preprint on GapMind for carbon sources, or view the source code.

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