Alignments for a candidate for rocA in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for rocA in Marinobacter adhaerens HP15

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate GFF2744 HP15_2688 trifunctional transcriptional regulator/proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase

Query= reanno::Marino:GFF2744
         (1209 letters)



>FitnessBrowser__Marino:GFF2744
          Length = 1209

 Score = 2369 bits (6139), Expect = 0.0
 Identities = 1209/1209 (100%), Positives = 1209/1209 (100%)

Query: 1    MRPQQSQTPELVDSRQAIRDYYLADEHKVIHEMIAGAQLSQAERDAISARAAELVRSVRK 60
            MRPQQSQTPELVDSRQAIRDYYLADEHKVIHEMIAGAQLSQAERDAISARAAELVRSVRK
Sbjct: 1    MRPQQSQTPELVDSRQAIRDYYLADEHKVIHEMIAGAQLSQAERDAISARAAELVRSVRK 60

Query: 61   NAKSTIMEKFLAEYGLTTKEGVALMCLAEALLRVPDNTTIHELIEDKITSGAWGTHVGKA 120
            NAKSTIMEKFLAEYGLTTKEGVALMCLAEALLRVPDNTTIHELIEDKITSGAWGTHVGKA
Sbjct: 61   NAKSTIMEKFLAEYGLTTKEGVALMCLAEALLRVPDNTTIHELIEDKITSGAWGTHVGKA 120

Query: 121  SSGLINTATVALLMTSNLLKDSERNTVGETLRKLLKRFGEPVIRTVAGQAMKEMGRQFVL 180
            SSGLINTATVALLMTSNLLKDSERNTVGETLRKLLKRFGEPVIRTVAGQAMKEMGRQFVL
Sbjct: 121  SSGLINTATVALLMTSNLLKDSERNTVGETLRKLLKRFGEPVIRTVAGQAMKEMGRQFVL 180

Query: 181  GRDIDEAQDEAKEYMAKGYTYSYDMLGEAARTDDDAKRYYDSYSNAIDSIAKASKGDVRK 240
            GRDIDEAQDEAKEYMAKGYTYSYDMLGEAARTDDDAKRYYDSYSNAIDSIAKASKGDVRK
Sbjct: 181  GRDIDEAQDEAKEYMAKGYTYSYDMLGEAARTDDDAKRYYDSYSNAIDSIAKASKGDVRK 240

Query: 241  NPGISVKLSALLARYEYGNKERVMNELLPRARELVKKAAAANMGFNIDAEEQDRLDLSLD 300
            NPGISVKLSALLARYEYGNKERVMNELLPRARELVKKAAAANMGFNIDAEEQDRLDLSLD
Sbjct: 241  NPGISVKLSALLARYEYGNKERVMNELLPRARELVKKAAAANMGFNIDAEEQDRLDLSLD 300

Query: 301  VIEELVADPELAGWDGFGVVVQAYGKRSSFVLDWLYGLAEKYDRKFMVRLVKGAYWDAEI 360
            VIEELVADPELAGWDGFGVVVQAYGKRSSFVLDWLYGLAEKYDRKFMVRLVKGAYWDAEI
Sbjct: 301  VIEELVADPELAGWDGFGVVVQAYGKRSSFVLDWLYGLAEKYDRKFMVRLVKGAYWDAEI 360

Query: 361  KRAQVMGLNGFPVFTRKACSDVSFLSCATKLLNMTNRIYPQFATHNAHSVSAILEMAKTK 420
            KRAQVMGLNGFPVFTRKACSDVSFLSCATKLLNMTNRIYPQFATHNAHSVSAILEMAKTK
Sbjct: 361  KRAQVMGLNGFPVFTRKACSDVSFLSCATKLLNMTNRIYPQFATHNAHSVSAILEMAKTK 420

Query: 421  GVDNYEFQRLHGMGESLHNEVLKVSGVPCRIYAPVGPHKDLLAYLVRRLLENGANSSFVN 480
            GVDNYEFQRLHGMGESLHNEVLKVSGVPCRIYAPVGPHKDLLAYLVRRLLENGANSSFVN
Sbjct: 421  GVDNYEFQRLHGMGESLHNEVLKVSGVPCRIYAPVGPHKDLLAYLVRRLLENGANSSFVN 480

Query: 481  QIVDKRITPEEIAKDPIVSVEEMGNNISSKAIVHPFKLFGDQRRNSKGWDITDPVTVNEI 540
            QIVDKRITPEEIAKDPIVSVEEMGNNISSKAIVHPFKLFGDQRRNSKGWDITDPVTVNEI
Sbjct: 481  QIVDKRITPEEIAKDPIVSVEEMGNNISSKAIVHPFKLFGDQRRNSKGWDITDPVTVNEI 540

Query: 541  EKGRGAYKDYRWKGGPLIAGEVAGTEIQVVRNPADPDDLVGHVTQASDADVDTAITSAAA 600
            EKGRGAYKDYRWKGGPLIAGEVAGTEIQVVRNPADPDDLVGHVTQASDADVDTAITSAAA
Sbjct: 541  EKGRGAYKDYRWKGGPLIAGEVAGTEIQVVRNPADPDDLVGHVTQASDADVDTAITSAAA 600

Query: 601  AFESWSAKSAEERAACVRKVGDLYEENYAELFALTTREAGKSLLDAVAEIREAVDFSQYY 660
            AFESWSAKSAEERAACVRKVGDLYEENYAELFALTTREAGKSLLDAVAEIREAVDFSQYY
Sbjct: 601  AFESWSAKSAEERAACVRKVGDLYEENYAELFALTTREAGKSLLDAVAEIREAVDFSQYY 660

Query: 661  ANEAIRYKDSGDARGVMCCISPWNFPLAIFTGQILANLAAGNTVVAKPAEQTSLLAIRAV 720
            ANEAIRYKDSGDARGVMCCISPWNFPLAIFTGQILANLAAGNTVVAKPAEQTSLLAIRAV
Sbjct: 661  ANEAIRYKDSGDARGVMCCISPWNFPLAIFTGQILANLAAGNTVVAKPAEQTSLLAIRAV 720

Query: 721  ELMHQAGIPKDAIQLVPGTGATVGAALTSDSRVSGVCFTGSTATAQRINKVMTENMAPDA 780
            ELMHQAGIPKDAIQLVPGTGATVGAALTSDSRVSGVCFTGSTATAQRINKVMTENMAPDA
Sbjct: 721  ELMHQAGIPKDAIQLVPGTGATVGAALTSDSRVSGVCFTGSTATAQRINKVMTENMAPDA 780

Query: 781  PLVAETGGLNAMIVDSTALPEQVVRDVLASSFQSAGQRCSALRMLYVQRDIADGLLEMLY 840
            PLVAETGGLNAMIVDSTALPEQVVRDVLASSFQSAGQRCSALRMLYVQRDIADGLLEMLY
Sbjct: 781  PLVAETGGLNAMIVDSTALPEQVVRDVLASSFQSAGQRCSALRMLYVQRDIADGLLEMLY 840

Query: 841  GAMEELGIGDPWLLSTDVGPVIDENARKKIVDHCEKFERNGKLLKKMKVPEKGLFVSPAV 900
            GAMEELGIGDPWLLSTDVGPVIDENARKKIVDHCEKFERNGKLLKKMKVPEKGLFVSPAV
Sbjct: 841  GAMEELGIGDPWLLSTDVGPVIDENARKKIVDHCEKFERNGKLLKKMKVPEKGLFVSPAV 900

Query: 901  LSVSGIEELEEEIFGPVLHVATFEAKNIDKVVDDINAKGYGLTFGIHSRVDRRVERITSR 960
            LSVSGIEELEEEIFGPVLHVATFEAKNIDKVVDDINAKGYGLTFGIHSRVDRRVERITSR
Sbjct: 901  LSVSGIEELEEEIFGPVLHVATFEAKNIDKVVDDINAKGYGLTFGIHSRVDRRVERITSR 960

Query: 961  IKVGNTYVNRNQIGAIVGSQPFGGEGLSGTGPKAGGPQYVRRFLKGETVEREADSNARKV 1020
            IKVGNTYVNRNQIGAIVGSQPFGGEGLSGTGPKAGGPQYVRRFLKGETVEREADSNARKV
Sbjct: 961  IKVGNTYVNRNQIGAIVGSQPFGGEGLSGTGPKAGGPQYVRRFLKGETVEREADSNARKV 1020

Query: 1021 DAKQLQKLIGQLDKLKASRPEARMDAIRPIFGNVPEPLDAHVEALPGPTGETNRLSNHAR 1080
            DAKQLQKLIGQLDKLKASRPEARMDAIRPIFGNVPEPLDAHVEALPGPTGETNRLSNHAR
Sbjct: 1021 DAKQLQKLIGQLDKLKASRPEARMDAIRPIFGNVPEPLDAHVEALPGPTGETNRLSNHAR 1080

Query: 1081 GVVLCLGPDKETALEQAGTALSQGNKVVVIAPGTQDVVDQANKAGLPIVGAQGLLEPEAL 1140
            GVVLCLGPDKETALEQAGTALSQGNKVVVIAPGTQDVVDQANKAGLPIVGAQGLLEPEAL
Sbjct: 1081 GVVLCLGPDKETALEQAGTALSQGNKVVVIAPGTQDVVDQANKAGLPIVGAQGLLEPEAL 1140

Query: 1141 ATIDGFEAVVSCGDQPLLKAYREALAKRDGALLPLITEHTLDQRFVIERHLCVDTTAAGG 1200
            ATIDGFEAVVSCGDQPLLKAYREALAKRDGALLPLITEHTLDQRFVIERHLCVDTTAAGG
Sbjct: 1141 ATIDGFEAVVSCGDQPLLKAYREALAKRDGALLPLITEHTLDQRFVIERHLCVDTTAAGG 1200

Query: 1201 NASLIAASE 1209
            NASLIAASE
Sbjct: 1201 NASLIAASE 1209


Lambda     K      H
   0.316    0.133    0.378 

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: 4129
Number of extensions: 157
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: 1209
Length of database: 1209
Length adjustment: 47
Effective length of query: 1162
Effective length of database: 1162
Effective search space:  1350244
Effective search space used:  1350244
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 59 (27.3 bits)

Align candidate GFF2744 HP15_2688 (trifunctional transcriptional regulator/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.3976225.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   3.1e-206  671.6   0.9     7e-206  670.5   0.2    1.9  2  FitnessBrowser__Marino:GFF2744  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__Marino:GFF2744  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  670.5   0.2    7e-206    7e-206       2     497 ..     518    1005 ..     517    1008 .. 0.98
   2 ?   -1.4   0.0     0.033     0.033     158     273 ..    1077    1179 ..    1070    1194 .. 0.70

  Alignments for each domain:
  == domain 1  score: 670.5 bits;  conditional E-value: 7e-206
                       TIGR01238    2 lygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdivGqvseadaaevqe 78  
                                      l+g+ r+ns+G d++   +++++e+   +  + +++  p++    +a  e+q v+npad++d+vG+v++a++a+v+ 
  FitnessBrowser__Marino:GFF2744  518 LFGDQRRNSKGWDITDPVTVNEIEKGRGAYKDYRWKGGPLI-AGEVAGTEIQVVRNPADPDDLVGHVTQASDADVDT 593 
                                      8****************************************.5668999**************************** PP

                       TIGR01238   79 avdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiaevreavdflryyakqvedvlde 155 
                                      a++sa aaf  wsa  a+eraa+++++ dl e++  el al+ reaGk+l +a+ae+reavdf +yya+++     +
  FitnessBrowser__Marino:GFF2744  594 AITSAAAAFESWSAKSAEERAACVRKVGDLYEENYAELFALTTREAGKSLLDAVAEIREAVDFSQYYANEA--IRYK 668 
                                      **********************************************************************9..4556 PP

                       TIGR01238  156 esakalGavvcispwnfplaiftGqiaaalaaGntviakpaeqtsliaaravellqeaGvpagviqllpGrGedvGa 232 
                                      +s  a+G++ cispwnfplaiftGqi a laaGntv+akpaeqtsl+a ravel+++aG+p  +iql+pG G++vGa
  FitnessBrowser__Marino:GFF2744  669 DSGDARGVMCCISPWNFPLAIFTGQILANLAAGNTVVAKPAEQTSLLAIRAVELMHQAGIPKDAIQLVPGTGATVGA 745 
                                      779************************************************************************** PP

                       TIGR01238  233 altsderiaGviftGstevarlinkalakredapvpliaetGGqnamivdstalaeqvvadvlasafdsaGqrcsal 309 
                                      altsd+r++Gv ftGst++a++ink +++  ++++pl+aetGG namivdstal+eqvv+dvlas+f+saGqrcsal
  FitnessBrowser__Marino:GFF2744  746 ALTSDSRVSGVCFTGSTATAQRINKVMTENMAPDAPLVAETGGLNAMIVDSTALPEQVVRDVLASSFQSAGQRCSAL 822 
                                      ***************************************************************************** PP

                       TIGR01238  310 rvlcvqedvadrvltlikGamdelkvgkpirlttdvGpvidaeakqnllahiekmkakakkvaqvkleddvesekgt 386 
                                      r+l+vq+d+ad +l+++ Gam+el +g p +l tdvGpvid++a+++++ h ek + ++k ++++k  +     kg 
  FitnessBrowser__Marino:GFF2744  823 RMLYVQRDIADGLLEMLYGAMEELGIGDPWLLSTDVGPVIDENARKKIVDHCEKFERNGKLLKKMKVPE-----KGL 894 
                                      **************************************************************9999887.....9** PP

                       TIGR01238  387 fvaptlfelddldelkkevfGpvlhvvrykadeldkvvdkinakGygltlGvhsrieetvrqiekrakvGnvyvnrn 463 
                                      fv+p ++ +  ++el++e+fGpvlhv  ++a+++dkvvd inakGyglt+G+hsr++  v +i++r+kvGn yvnrn
  FitnessBrowser__Marino:GFF2744  895 FVSPAVLSVSGIEELEEEIFGPVLHVATFEAKNIDKVVDDINAKGYGLTFGIHSRVDRRVERITSRIKVGNTYVNRN 971 
                                      ***************************************************************************** PP

                       TIGR01238  464 lvGavvGvqpfGGeGlsGtGpkaGGplylyrltr 497 
                                      ++Ga+vG qpfGGeGlsGtGpkaGGp y+ r+++
  FitnessBrowser__Marino:GFF2744  972 QIGAIVGSQPFGGEGLSGTGPKAGGPQYVRRFLK 1005
                                      *******************************987 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.033
                       TIGR01238  158 akalGavvcispwnfplaiftGqiaaalaaGntvia.kpaeqtsliaaravellqeaGvpagviqllpGrGedvGaa 233 
                                       +a+G+v+c+ p        + q  +al  Gn v+   p  q        v+  ++aG+p    q l+        a
  FitnessBrowser__Marino:GFF2744 1077 NHARGVVLCLGPDKE---TALEQAGTALSQGNKVVViAPGTQD------VVDQANKAGLPIVGAQGLLE-----PEA 1139
                                      567777777777543...3456778888888877641344432......34445678888766665553.....346 PP

                       TIGR01238  234 ltsderiaGviftGstevarlinkalakredapvpliaet 273 
                                      l++ +  + v+  G     +  ++alakr+ a  pli+e 
  FitnessBrowser__Marino:GFF2744 1140 LATIDGFEAVVSCGDQPLLKAYREALAKRDGALLPLITEH 1179
                                      7777788888888999999999999999999999999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (500 nodes)
Target sequences:                          1  (1209 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 43.91
//
[ok]

This GapMind analysis is from Apr 09 2024. 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 2024 update 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