GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocA 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)



>FitnessBrowser__Korea:Ga0059261_3926
          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.31461.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 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 25.27
//
[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:

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