GapMind for catabolism of small carbon sources

 

Alignments for a candidate for putA in Pseudomonas stutzeri RCH2

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate GFF3021 Psest_3079 delta-1-pyrroline-5-carboxylate dehydrogenase (PutA C-terminal domain)

Query= reanno::psRCH2:GFF3021
         (1053 letters)



>FitnessBrowser__psRCH2:GFF3021
          Length = 1053

 Score = 2078 bits (5384), Expect = 0.0
 Identities = 1053/1053 (100%), Positives = 1053/1053 (100%)

Query: 1    MFKAGHVLDGAFANQKAAEFFPAISANYSVDEAQYLTELLQLADPGEAGIAAIRERARSL 60
            MFKAGHVLDGAFANQKAAEFFPAISANYSVDEAQYLTELLQLADPGEAGIAAIRERARSL
Sbjct: 1    MFKAGHVLDGAFANQKAAEFFPAISANYSVDEAQYLTELLQLADPGEAGIAAIRERARSL 60

Query: 61   IEAVRGRDNAVDTLDALLRQYSLDTQEGLMLMCLAEALLRVPDAATADALIRDKLNAAEW 120
            IEAVRGRDNAVDTLDALLRQYSLDTQEGLMLMCLAEALLRVPDAATADALIRDKLNAAEW
Sbjct: 61   IEAVRGRDNAVDTLDALLRQYSLDTQEGLMLMCLAEALLRVPDAATADALIRDKLNAAEW 120

Query: 121  ERHLGQSDNVLVNFAAWGLVMTGKVVDPETADGRPKNVIGRLLKRSGEPVIRGAMNQAMK 180
            ERHLGQSDNVLVNFAAWGLVMTGKVVDPETADGRPKNVIGRLLKRSGEPVIRGAMNQAMK
Sbjct: 121  ERHLGQSDNVLVNFAAWGLVMTGKVVDPETADGRPKNVIGRLLKRSGEPVIRGAMNQAMK 180

Query: 181  LMGKQFVLGRTISEALKNGRPEREKGYTYSFDMLGEAALTAEDAAKYMADYRQAVETVGA 240
            LMGKQFVLGRTISEALKNGRPEREKGYTYSFDMLGEAALTAEDAAKYMADYRQAVETVGA
Sbjct: 181  LMGKQFVLGRTISEALKNGRPEREKGYTYSFDMLGEAALTAEDAAKYMADYRQAVETVGA 240

Query: 241  EPQVGKGPRPSVSIKLSALHPRYELAQRERVLTELFGSVRELAILARRLNVGITIDAEEA 300
            EPQVGKGPRPSVSIKLSALHPRYELAQRERVLTELFGSVRELAILARRLNVGITIDAEEA
Sbjct: 241  EPQVGKGPRPSVSIKLSALHPRYELAQRERVLTELFGSVRELAILARRLNVGITIDAEEA 300

Query: 301  DRLELSLELYEKLLRDPAIAGWGEFGLVIQAYSKRCLPVLVWLTLLGRELGERIPLRLVK 360
            DRLELSLELYEKLLRDPAIAGWGEFGLVIQAYSKRCLPVLVWLTLLGRELGERIPLRLVK
Sbjct: 301  DRLELSLELYEKLLRDPAIAGWGEFGLVIQAYSKRCLPVLVWLTLLGRELGERIPLRLVK 360

Query: 361  GAYWDSEIKQCQVQGLDGYPVYTRKEGTDTSYLACARYLLSEHTRGVIYPQFASHNAHTV 420
            GAYWDSEIKQCQVQGLDGYPVYTRKEGTDTSYLACARYLLSEHTRGVIYPQFASHNAHTV
Sbjct: 361  GAYWDSEIKQCQVQGLDGYPVYTRKEGTDTSYLACARYLLSEHTRGVIYPQFASHNAHTV 420

Query: 421  SCILAMAEETAQPREFEFQRLHGMGDALYDTVIEKYARNVRIYAPVGAHKDLLPYLVRRL 480
            SCILAMAEETAQPREFEFQRLHGMGDALYDTVIEKYARNVRIYAPVGAHKDLLPYLVRRL
Sbjct: 421  SCILAMAEETAQPREFEFQRLHGMGDALYDTVIEKYARNVRIYAPVGAHKDLLPYLVRRL 480

Query: 481  LENGANSSFVHQLVDPRVPVESLIDHPVTQLRRFAAPGNPRIPLPPALFGNRKNSQGINM 540
            LENGANSSFVHQLVDPRVPVESLIDHPVTQLRRFAAPGNPRIPLPPALFGNRKNSQGINM
Sbjct: 481  LENGANSSFVHQLVDPRVPVESLIDHPVTQLRRFAAPGNPRIPLPPALFGNRKNSQGINM 540

Query: 541  NIQNQWTELASAYQPFLERQWQAAPVISGRTLAGTPSEVRCPYELNKVVGQAQFASADQA 600
            NIQNQWTELASAYQPFLERQWQAAPVISGRTLAGTPSEVRCPYELNKVVGQAQFASADQA
Sbjct: 541  NIQNQWTELASAYQPFLERQWQAAPVISGRTLAGTPSEVRCPYELNKVVGQAQFASADQA 600

Query: 601  RQAIDRLAAYWPIWNATPVEARAAVLERLGDLLEQHRAELMALCTVEAGKSLQDGIDEVR 660
            RQAIDRLAAYWPIWNATPVEARAAVLERLGDLLEQHRAELMALCTVEAGKSLQDGIDEVR
Sbjct: 601  RQAIDRLAAYWPIWNATPVEARAAVLERLGDLLEQHRAELMALCTVEAGKSLQDGIDEVR 660

Query: 661  EAVDFCRYYAQQARLKLGREELKGPTGERNELFHEGRGVFVCVSPWNFPLAIYLGQITAA 720
            EAVDFCRYYAQQARLKLGREELKGPTGERNELFHEGRGVFVCVSPWNFPLAIYLGQITAA
Sbjct: 661  EAVDFCRYYAQQARLKLGREELKGPTGERNELFHEGRGVFVCVSPWNFPLAIYLGQITAA 720

Query: 721  LVAGNTVLAKPAEQTSLIAARALELMFEAGLPQEAIAFLPGDGATLGGVFCRDPRVVGVC 780
            LVAGNTVLAKPAEQTSLIAARALELMFEAGLPQEAIAFLPGDGATLGGVFCRDPRVVGVC
Sbjct: 721  LVAGNTVLAKPAEQTSLIAARALELMFEAGLPQEAIAFLPGDGATLGGVFCRDPRVVGVC 780

Query: 781  FTGSTDTARIINRQLAEKEGPIATLIAETGGQNAMIVDSTALPEQVIKDAVGSAFTSAGQ 840
            FTGSTDTARIINRQLAEKEGPIATLIAETGGQNAMIVDSTALPEQVIKDAVGSAFTSAGQ
Sbjct: 781  FTGSTDTARIINRQLAEKEGPIATLIAETGGQNAMIVDSTALPEQVIKDAVGSAFTSAGQ 840

Query: 841  RCSALRVLYVQRDIADRVIDLLKGAMAELRVGPTHLRENDIGPVIDQEAREGLLAHIQQL 900
            RCSALRVLYVQRDIADRVIDLLKGAMAELRVGPTHLRENDIGPVIDQEAREGLLAHIQQL
Sbjct: 841  RCSALRVLYVQRDIADRVIDLLKGAMAELRVGPTHLRENDIGPVIDQEAREGLLAHIQQL 900

Query: 901  KSEGRLIAEATVPAGLNGHFVAPVAFEIDGIHQLKKEHFGPVLHVVRYDAADLEKVVAAI 960
            KSEGRLIAEATVPAGLNGHFVAPVAFEIDGIHQLKKEHFGPVLHVVRYDAADLEKVVAAI
Sbjct: 901  KSEGRLIAEATVPAGLNGHFVAPVAFEIDGIHQLKKEHFGPVLHVVRYDAADLEKVVAAI 960

Query: 961  NGTGYGLTLGVHSRNEETAERIEQLARVGNLYVNRNQIGAVVGVQPFGGCRLSGTGPKAG 1020
            NGTGYGLTLGVHSRNEETAERIEQLARVGNLYVNRNQIGAVVGVQPFGGCRLSGTGPKAG
Sbjct: 961  NGTGYGLTLGVHSRNEETAERIEQLARVGNLYVNRNQIGAVVGVQPFGGCRLSGTGPKAG 1020

Query: 1021 GPSYLLRFANERTTSTNTTAVGGNASLLSLGDD 1053
            GPSYLLRFANERTTSTNTTAVGGNASLLSLGDD
Sbjct: 1021 GPSYLLRFANERTTSTNTTAVGGNASLLSLGDD 1053


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: 3243
Number of extensions: 94
Number of successful extensions: 1
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: 1053
Length of database: 1053
Length adjustment: 45
Effective length of query: 1008
Effective length of database: 1008
Effective search space:  1016064
Effective search space used:  1016064
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: 58 (26.9 bits)

Align candidate GFF3021 Psest_3079 (delta-1-pyrroline-5-carboxylate dehydrogenase (PutA C-terminal domain))
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.20994.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   3.4e-211  688.0   0.2     5e-211  687.4   0.2    1.2  1  lcl|FitnessBrowser__psRCH2:GFF3021  Psest_3079 delta-1-pyrroline-5-c


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF3021  Psest_3079 delta-1-pyrroline-5-carboxylate dehydrogenase (PutA C-terminal domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  687.4   0.2    5e-211    5e-211       2     497 ..     528    1030 ..     527    1033 .. 0.98

  Alignments for each domain:
  == domain 1  score: 687.4 bits;  conditional E-value: 5e-211
                           TIGR01238    2 lygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdivGqvseadaa 74  
                                          l+g+ rkns+G++++++++  +l +  +  +++++qaap++++++ a g    v+ p++ +++vGq ++a+a+
  lcl|FitnessBrowser__psRCH2:GFF3021  528 LFGN-RKNSQGINMNIQNQWTELASAYQPFLERQWQAAPVISGRTLA-GTPSEVRCPYELNKVVGQAQFASAD 598 
                                          7898.************************************877766.66678******************** PP

                           TIGR01238   75 evqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiaevreavdflryyak 147 
                                          ++++a+d   a  ++w+at+ + raa+lerl dlle+h  el+al+  eaGk+l++ i+evreavdf+ryya+
  lcl|FitnessBrowser__psRCH2:GFF3021  599 QARQAIDRLAAYWPIWNATPVEARAAVLERLGDLLEQHRAELMALCTVEAGKSLQDGIDEVREAVDFCRYYAQ 671 
                                          ************************************************************************* PP

                           TIGR01238  148 qvedvldeesaka............lGavvcispwnfplaiftGqiaaalaaGntviakpaeqtsliaarave 208 
                                          q++ +l++e  k             +G++vc+spwnfplai++Gqi+aal+aGntv+akpaeqtsliaara+e
  lcl|FitnessBrowser__psRCH2:GFF3021  672 QARLKLGREELKGptgernelfhegRGVFVCVSPWNFPLAIYLGQITAALVAGNTVLAKPAEQTSLIAARALE 744 
                                          *********99989*********************************************************** PP

                           TIGR01238  209 llqeaGvpagviqllpGrGedvGaaltsderiaGviftGstevarlinkalakredapvpliaetGGqnamiv 281 
                                          l+ eaG+p  +i +lpG G+++G  +  d+r+ Gv ftGst++ar in++la++e + ++liaetGGqnamiv
  lcl|FitnessBrowser__psRCH2:GFF3021  745 LMFEAGLPQEAIAFLPGDGATLGGVFCRDPRVVGVCFTGSTDTARIINRQLAEKEGPIATLIAETGGQNAMIV 817 
                                          ************************************************************************* PP

                           TIGR01238  282 dstalaeqvvadvlasafdsaGqrcsalrvlcvqedvadrvltlikGamdelkvgkpirlttdvGpvidaeak 354 
                                          dstal+eqv++d + saf saGqrcsalrvl+vq+d+adrv++l+kGam el+vg  ++ + d+Gpvid+ea+
  lcl|FitnessBrowser__psRCH2:GFF3021  818 DSTALPEQVIKDAVGSAFTSAGQRCSALRVLYVQRDIADRVIDLLKGAMAELRVGPTHLRENDIGPVIDQEAR 890 
                                          ************************************************************************* PP

                           TIGR01238  355 qnllahiekmkakakkvaqvkleddvesekgtfvaptlfelddldelkkevfGpvlhvvrykadeldkvvdki 427 
                                          + llahi+++k+ ++ +a+++  +     +g fvap++fe+d +++lkke fGpvlhvvry a +l+kvv  i
  lcl|FitnessBrowser__psRCH2:GFF3021  891 EGLLAHIQQLKSEGRLIAEATVPA---GLNGHFVAPVAFEIDGIHQLKKEHFGPVLHVVRYDAADLEKVVAAI 960 
                                          *********************998...678******************************************* PP

                           TIGR01238  428 nakGygltlGvhsrieetvrqiekrakvGnvyvnrnlvGavvGvqpfGGeGlsGtGpkaGGplylyrltr 497 
                                          n +GygltlGvhsr+eet  +ie+ a+vGn+yvnrn++GavvGvqpfGG  lsGtGpkaGGp yl r+ +
  lcl|FitnessBrowser__psRCH2:GFF3021  961 NGTGYGLTLGVHSRNEETAERIEQLARVGNLYVNRNQIGAVVGVQPFGGCRLSGTGPKAGGPSYLLRFAN 1030
                                          *******************************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (500 nodes)
Target sequences:                          1  (1053 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: 17.88
//
[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