Alignments for a candidate for mmsA in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Pseudomonas stutzeri RCH2

Align Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized)
to candidate GFF2388 Psest_2436 methylmalonic acid semialdehyde dehydrogenase

Query= reanno::psRCH2:GFF2388
         (503 letters)



>FitnessBrowser__psRCH2:GFF2388
          Length = 503

 Score =  999 bits (2583), Expect = 0.0
 Identities = 503/503 (100%), Positives = 503/503 (100%)

Query: 1   MTTSSSIPTVKLLIDGEFIESTTQDWRDVVNPATQEVLARVPFATAEEIDRAVASGQKAF 60
           MTTSSSIPTVKLLIDGEFIESTTQDWRDVVNPATQEVLARVPFATAEEIDRAVASGQKAF
Sbjct: 1   MTTSSSIPTVKLLIDGEFIESTTQDWRDVVNPATQEVLARVPFATAEEIDRAVASGQKAF 60

Query: 61  KTWRKTPIGARARIFLKYQQLIRENMKELAAILTAEQGKTLADAEGDVFRGLEVVEHAAG 120
           KTWRKTPIGARARIFLKYQQLIRENMKELAAILTAEQGKTLADAEGDVFRGLEVVEHAAG
Sbjct: 61  KTWRKTPIGARARIFLKYQQLIRENMKELAAILTAEQGKTLADAEGDVFRGLEVVEHAAG 120

Query: 121 IGNLQLGELANNVAAGVDTYTLLQPLGVCAGITPFNFPAMIPLWMFPMAIATGNTFVLKP 180
           IGNLQLGELANNVAAGVDTYTLLQPLGVCAGITPFNFPAMIPLWMFPMAIATGNTFVLKP
Sbjct: 121 IGNLQLGELANNVAAGVDTYTLLQPLGVCAGITPFNFPAMIPLWMFPMAIATGNTFVLKP 180

Query: 181 SEQDPMVTMRLCELALEAGVPPGVLNVVHGGPDVVNAICDHPDIKAVSFVGSTKVGTHVY 240
           SEQDPMVTMRLCELALEAGVPPGVLNVVHGGPDVVNAICDHPDIKAVSFVGSTKVGTHVY
Sbjct: 181 SEQDPMVTMRLCELALEAGVPPGVLNVVHGGPDVVNAICDHPDIKAVSFVGSTKVGTHVY 240

Query: 241 NRASQAGKRVQCMMGAKNHAIVLPDAHKEQTLNNLAGAAFGAAGQRCMALSVVVLVGEAQ 300
           NRASQAGKRVQCMMGAKNHAIVLPDAHKEQTLNNLAGAAFGAAGQRCMALSVVVLVGEAQ
Sbjct: 241 NRASQAGKRVQCMMGAKNHAIVLPDAHKEQTLNNLAGAAFGAAGQRCMALSVVVLVGEAQ 300

Query: 301 AWIPDLVAKAQTLKVNAGVEAGTDVGPLVSCAALDRVSGLIERGVREGAKLELDGRNPSV 360
           AWIPDLVAKAQTLKVNAGVEAGTDVGPLVSCAALDRVSGLIERGVREGAKLELDGRNPSV
Sbjct: 301 AWIPDLVAKAQTLKVNAGVEAGTDVGPLVSCAALDRVSGLIERGVREGAKLELDGRNPSV 360

Query: 361 SGYENGNFVGPTIFSGVTREMSVYQEEIFGPVLCVMAAATMDEAIELINANPNGNGTAIF 420
           SGYENGNFVGPTIFSGVTREMSVYQEEIFGPVLCVMAAATMDEAIELINANPNGNGTAIF
Sbjct: 361 SGYENGNFVGPTIFSGVTREMSVYQEEIFGPVLCVMAAATMDEAIELINANPNGNGTAIF 420

Query: 421 TRSGAAARHFQEEIDVGQVGINVPIPVPVPMFSFTGSRASKLGDLGPYGKQVVQFYTQTK 480
           TRSGAAARHFQEEIDVGQVGINVPIPVPVPMFSFTGSRASKLGDLGPYGKQVVQFYTQTK
Sbjct: 421 TRSGAAARHFQEEIDVGQVGINVPIPVPVPMFSFTGSRASKLGDLGPYGKQVVQFYTQTK 480

Query: 481 TITERWFDENEVGGPVNTTINLK 503
           TITERWFDENEVGGPVNTTINLK
Sbjct: 481 TITERWFDENEVGGPVNTTINLK 503


Lambda     K      H
   0.318    0.134    0.394 

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: 951
Number of extensions: 28
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: 503
Length of database: 503
Length adjustment: 34
Effective length of query: 469
Effective length of database: 469
Effective search space:   219961
Effective search space used:   219961
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 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate GFF2388 Psest_2436 (methylmalonic acid semialdehyde dehydrogenase)
to HMM TIGR01722 (mmsA: methylmalonate-semialdehyde dehydrogenase (acylating) (EC 1.2.1.27))

# 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/TIGR01722.hmm
# target sequence database:        /tmp/gapView.2961504.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01722  [M=477]
Accession:   TIGR01722
Description: MMSDH: methylmalonate-semialdehyde dehydrogenase (acylating)
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   4.1e-227  740.4   1.9   4.6e-227  740.2   1.9    1.0  1  FitnessBrowser__psRCH2:GFF2388  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__psRCH2:GFF2388  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  740.2   1.9  4.6e-227  4.6e-227       1     477 []      10     486 ..      10     486 .. 1.00

  Alignments for each domain:
  == domain 1  score: 740.2 bits;  conditional E-value: 4.6e-227
                       TIGR01722   1 vkhlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryqallkehrde 79 
                                     vk+lidG+f+e++++ + +v npat+evla+v++a+aee+d avas +++f +w++t++  rar++l+yq+l++e+ +e
  FitnessBrowser__psRCH2:GFF2388  10 VKLLIDGEFIESTTQDWRDVVNPATQEVLARVPFATAEEIDRAVASGQKAFKTWRKTPIGARARIFLKYQQLIRENMKE 88 
                                     899**************************************************************************** PP

                       TIGR01722  80 iaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGvvaGitpfnfpamiplwmfp 158
                                     +a +++aeqGktl+da+Gdv+rGlevveha ++  l lGe+ ++va  vd+y++ qplGv+aGitpfnfpamiplwmfp
  FitnessBrowser__psRCH2:GFF2388  89 LAAILTAEQGKTLADAEGDVFRGLEVVEHAAGIGNLQLGELANNVAAGVDTYTLLQPLGVCAGITPFNFPAMIPLWMFP 167
                                     ******************************************************************************* PP

                       TIGR01722 159 laiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdrllehpdvkavsfvGsvavgeyiyetgsah 237
                                     +aia Gntfvlkpse++p  +++l el +eaG+p GvlnvvhG+ + v+ +++hpd+kavsfvGs++vg ++y+++s+ 
  FitnessBrowser__psRCH2:GFF2388 168 MAIATGNTFVLKPSEQDPMVTMRLCELALEAGVPPGVLNVVHGGPDVVNAICDHPDIKAVSFVGSTKVGTHVYNRASQA 246
                                     ******************************************************************************* PP

                       TIGR01722 238 gkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqrcmaisaavlvGaakelveeireraekvrvgagddpgael 316
                                     gkrvq+++Gaknh++vlpda+ke++l++l gaa+GaaGqrcma+s++vlvG+a+ ++++++ +a+ ++v+ag ++g+++
  FitnessBrowser__psRCH2:GFF2388 247 GKRVQCMMGAKNHAIVLPDAHKEQTLNNLAGAAFGAAGQRCMALSVVVLVGEAQAWIPDLVAKAQTLKVNAGVEAGTDV 325
                                     ******************************************************************************* PP

                       TIGR01722 317 GplitkqakervasliasgakeGaevlldGrgykveGyeeGnfvGitllervkpdmkiykeeifGpvlvvleadtleea 395
                                     Gpl++ +a +rv+ li+ g++eGa++ ldGr+  v Gye+GnfvG+t++++v  +m++y+eeifGpvl+v+ a t++ea
  FitnessBrowser__psRCH2:GFF2388 326 GPLVSCAALDRVSGLIERGVREGAKLELDGRNPSVSGYENGNFVGPTIFSGVTREMSVYQEEIFGPVLCVMAAATMDEA 404
                                     ******************************************************************************* PP

                       TIGR01722 396 iklinespyGnGtaiftsdGaaarkfqheievGqvGvnvpipvplpffsftGwkdslfGdlhiyGkqGvrfytrlktvt 474
                                     i+lin++p GnGtaift++Gaaar+fq ei+vGqvG+nvpipvp+p+fsftG+++s  Gdl  yGkq v+fyt++kt+t
  FitnessBrowser__psRCH2:GFF2388 405 IELINANPNGNGTAIFTRSGAAARHFQEEIDVGQVGINVPIPVPVPMFSFTGSRASKLGDLGPYGKQVVQFYTQTKTIT 483
                                     ******************************************************************************* PP

                       TIGR01722 475 arw 477
                                      rw
  FitnessBrowser__psRCH2:GFF2388 484 ERW 486
                                     *** PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (477 nodes)
Target sequences:                          1  (503 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 35.32
//
[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