Alignments for a candidate for mmsA in Pseudomonas litoralis 2SM5

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Pseudomonas litoralis 2SM5

Align Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized)
to candidate WP_090273754.1 BLU11_RS12285 CoA-acylating methylmalonate-semialdehyde dehydrogenase

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



>NCBI__GCF_900105005.1:WP_090273754.1
          Length = 502

 Score =  844 bits (2180), Expect = 0.0
 Identities = 406/501 (81%), Positives = 462/501 (92%)

Query: 3   TSSSIPTVKLLIDGEFIESTTQDWRDVVNPATQEVLARVPFATAEEIDRAVASGQKAFKT 62
           +++++PTVKLLI+GEF+ES T  WRDV+NPATQEVLARVPFAT +EI+ AVAS ++AFKT
Sbjct: 2   SNNNLPTVKLLINGEFVESKTDQWRDVINPATQEVLARVPFATQDEINAAVASAKEAFKT 61

Query: 63  WRKTPIGARARIFLKYQQLIRENMKELAAILTAEQGKTLADAEGDVFRGLEVVEHAAGIG 122
           WRKTPIGARARIFLKYQQLIREN+KELAAILTAEQGKT+ADAEGDVFRGLEVVEHA+ +G
Sbjct: 62  WRKTPIGARARIFLKYQQLIRENIKELAAILTAEQGKTMADAEGDVFRGLEVVEHASAVG 121

Query: 123 NLQLGELANNVAAGVDTYTLLQPLGVCAGITPFNFPAMIPLWMFPMAIATGNTFVLKPSE 182
           NLQLGELANNVA GVDTYTLLQPLGVCAGITPFNFPAMIPLWMFPMAIATGNTFVLKPSE
Sbjct: 122 NLQLGELANNVAGGVDTYTLLQPLGVCAGITPFNFPAMIPLWMFPMAIATGNTFVLKPSE 181

Query: 183 QDPMVTMRLCELALEAGVPPGVLNVVHGGPDVVNAICDHPDIKAVSFVGSTKVGTHVYNR 242
           QDPMVTMRL ELALEAG+PPGVLNV+HGG D VN +CDHPDIKAVSFVGST VGTHVYNR
Sbjct: 182 QDPMVTMRLVELALEAGIPPGVLNVIHGGVDAVNGVCDHPDIKAVSFVGSTHVGTHVYNR 241

Query: 243 ASQAGKRVQCMMGAKNHAIVLPDAHKEQTLNNLAGAAFGAAGQRCMALSVVVLVGEAQAW 302
           ASQAGKRVQCMMGAKNHA+++PDA+KEQTLNNL GAAFGAAGQRCMAL V++LVGE++ W
Sbjct: 242 ASQAGKRVQCMMGAKNHAVIMPDANKEQTLNNLIGAAFGAAGQRCMALPVIILVGESRNW 301

Query: 303 IPDLVAKAQTLKVNAGVEAGTDVGPLVSCAALDRVSGLIERGVREGAKLELDGRNPSVSG 362
           +P+L  KA+TLKV+AG+EAGTDVGP++S +AL+RV+GLI++G+ EGA+L LDGRNP+V+G
Sbjct: 302 LPELARKAETLKVSAGIEAGTDVGPVISTSALERVNGLIQKGIDEGAELVLDGRNPNVAG 361

Query: 363 YENGNFVGPTIFSGVTREMSVYQEEIFGPVLCVMAAATMDEAIELINANPNGNGTAIFTR 422
           Y +GNFVGPTIF+GV   M+VY EEIFGPVLCVM A ++DEAI++INANPNGNGTAIFTR
Sbjct: 362 YADGNFVGPTIFAGVKPGMTVYDEEIFGPVLCVMQADSLDEAIDIINANPNGNGTAIFTR 421

Query: 423 SGAAARHFQEEIDVGQVGINVPIPVPVPMFSFTGSRASKLGDLGPYGKQVVQFYTQTKTI 482
           SG  AR FQE+IDVGQVGINVPIPVPVP+FSF+GSR SKLGDLGPYGKQV+ FYTQTKTI
Sbjct: 422 SGGIARRFQEDIDVGQVGINVPIPVPVPLFSFSGSRGSKLGDLGPYGKQVILFYTQTKTI 481

Query: 483 TERWFDENEVGGPVNTTINLK 503
           T RWFD++E    VNTTI LK
Sbjct: 482 TARWFDDDEQAAAVNTTITLK 502


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: 840
Number of extensions: 29
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: 502
Length adjustment: 34
Effective length of query: 469
Effective length of database: 468
Effective search space:   219492
Effective search space used:   219492
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 WP_090273754.1 BLU11_RS12285 (CoA-acylating methylmalonate-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.3590008.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.9e-228  743.0   1.3   7.8e-228  742.8   1.3    1.0  1  NCBI__GCF_900105005.1:WP_090273754.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900105005.1:WP_090273754.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  742.8   1.3  7.8e-228  7.8e-228       1     477 []       9     485 ..       9     485 .. 1.00

  Alignments for each domain:
  == domain 1  score: 742.8 bits;  conditional E-value: 7.8e-228
                             TIGR01722   1 vkhlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryqall 73 
                                           vk+li+G+fve+k+d++ +v npat+evla+v++a+++e++aavasa+e+f +w++t++  rar++l+yq+l+
  NCBI__GCF_900105005.1:WP_090273754.1   9 VKLLINGEFVESKTDQWRDVINPATQEVLARVPFATQDEINAAVASAKEAFKTWRKTPIGARARIFLKYQQLI 81 
                                           899********************************************************************** PP

                             TIGR01722  74 kehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGvvaGitpf 146
                                           +e+ +e+a +++aeqGkt++da+Gdv+rGlevveha +v  l lGe+ ++va  vd+y++ qplGv+aGitpf
  NCBI__GCF_900105005.1:WP_090273754.1  82 RENIKELAAILTAEQGKTMADAEGDVFRGLEVVEHASAVGNLQLGELANNVAGGVDTYTLLQPLGVCAGITPF 154
                                           ************************************************************************* PP

                             TIGR01722 147 nfpamiplwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdrllehpdvkavs 219
                                           nfpamiplwmfp+aia Gntfvlkpse++p  +++l el +eaG+p Gvlnv+hG+ +av+ +++hpd+kavs
  NCBI__GCF_900105005.1:WP_090273754.1 155 NFPAMIPLWMFPMAIATGNTFVLKPSEQDPMVTMRLVELALEAGIPPGVLNVIHGGVDAVNGVCDHPDIKAVS 227
                                           ************************************************************************* PP

                             TIGR01722 220 fvGsvavgeyiyetgsahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqrcmaisaavlvGaake 292
                                           fvGs++vg ++y+++s+ gkrvq+++Gaknh+v++pda+ke++l++l+gaa+GaaGqrcma+ +++lvG+ ++
  NCBI__GCF_900105005.1:WP_090273754.1 228 FVGSTHVGTHVYNRASQAGKRVQCMMGAKNHAVIMPDANKEQTLNNLIGAAFGAAGQRCMALPVIILVGESRN 300
                                           ************************************************************************* PP

                             TIGR01722 293 lveeireraekvrvgagddpgaelGplitkqakervasliasgakeGaevlldGrgykveGyeeGnfvGitll 365
                                           +++e+  +ae ++v+ag ++g+++Gp+i+ +a erv+ li++g++eGae++ldGr+ +v Gy +GnfvG+t++
  NCBI__GCF_900105005.1:WP_090273754.1 301 WLPELARKAETLKVSAGIEAGTDVGPVISTSALERVNGLIQKGIDEGAELVLDGRNPNVAGYADGNFVGPTIF 373
                                           ************************************************************************* PP

                             TIGR01722 366 ervkpdmkiykeeifGpvlvvleadtleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGvnvpipv 438
                                           ++vkp m++y eeifGpvl+v++ad+l+eai +in++p GnGtaift++G+ ar+fq +i+vGqvG+nvpipv
  NCBI__GCF_900105005.1:WP_090273754.1 374 AGVKPGMTVYDEEIFGPVLCVMQADSLDEAIDIINANPNGNGTAIFTRSGGIARRFQEDIDVGQVGINVPIPV 446
                                           ************************************************************************* PP

                             TIGR01722 439 plpffsftGwkdslfGdlhiyGkqGvrfytrlktvtarw 477
                                           p+p+fsf+G+++s  Gdl  yGkq + fyt++kt+tarw
  NCBI__GCF_900105005.1:WP_090273754.1 447 PVPLFSFSGSRGSKLGDLGPYGKQVILFYTQTKTITARW 485
                                           *************************************** PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (477 nodes)
Target sequences:                          1  (502 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.09
# Mc/sec: 2.58
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
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Protein sequences (fasta format)
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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