Alignments for a candidate for mmsA in Stenotrophomonas chelatiphaga DSM 21508

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Stenotrophomonas chelatiphaga DSM 21508

Align Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized)
to candidate WP_057507564.1 ABB28_RS04920 methylmalonate-semialdehyde dehydrogenase (CoA acylating)

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



>NCBI__GCF_001431535.1:WP_057507564.1
          Length = 501

 Score =  823 bits (2125), Expect = 0.0
 Identities = 400/496 (80%), Positives = 450/496 (90%)

Query: 8   PTVKLLIDGEFIESTTQDWRDVVNPATQEVLARVPFATAEEIDRAVASGQKAFKTWRKTP 67
           P ++LLIDG+FIES+T  W+DVVNPATQ+VLA+VPFAT  E+D AVA+ ++AFKTWRKTP
Sbjct: 6   PRIRLLIDGQFIESSTAHWQDVVNPATQDVLAQVPFATTSEVDDAVAAAKEAFKTWRKTP 65

Query: 68  IGARARIFLKYQQLIRENMKELAAILTAEQGKTLADAEGDVFRGLEVVEHAAGIGNLQLG 127
           IG RARIFLKYQQLIRENM ELA  L+AEQGKT+ DAEGDVFRGLEVVEHAA IGNLQLG
Sbjct: 66  IGTRARIFLKYQQLIRENMSELAHTLSAEQGKTVPDAEGDVFRGLEVVEHAAAIGNLQLG 125

Query: 128 ELANNVAAGVDTYTLLQPLGVCAGITPFNFPAMIPLWMFPMAIATGNTFVLKPSEQDPMV 187
           ELANNVA GVDTYTL+QPLGVCAGITPFNFPAMIPLWMFPMAIATGNTFVLKPSEQDPMV
Sbjct: 126 ELANNVANGVDTYTLMQPLGVCAGITPFNFPAMIPLWMFPMAIATGNTFVLKPSEQDPMV 185

Query: 188 TMRLCELALEAGVPPGVLNVVHGGPDVVNAICDHPDIKAVSFVGSTKVGTHVYNRASQAG 247
           TMRL ELALEAG+P GVLNVVHGG +VVNAICDHPDIKAVSFVGST+VGTHVYNRAS AG
Sbjct: 186 TMRLVELALEAGIPKGVLNVVHGGEEVVNAICDHPDIKAVSFVGSTRVGTHVYNRASLAG 245

Query: 248 KRVQCMMGAKNHAIVLPDAHKEQTLNNLAGAAFGAAGQRCMALSVVVLVGEAQAWIPDLV 307
           KRVQCMMGAKNHA+VLPDA+KEQTLN + GAAFGAAGQRCMA S +VLVGEA++W+PDLV
Sbjct: 246 KRVQCMMGAKNHAVVLPDANKEQTLNAMVGAAFGAAGQRCMAASTLVLVGEARSWVPDLV 305

Query: 308 AKAQTLKVNAGVEAGTDVGPLVSCAALDRVSGLIERGVREGAKLELDGRNPSVSGYENGN 367
           AKA+TLKV+AG  AGTDVGP++SC+A +RV GLI  G+ +GA L+LDGRNP V G+E GN
Sbjct: 306 AKAKTLKVSAGSVAGTDVGPVISCSARERVEGLIASGLEQGATLDLDGRNPQVDGFEKGN 365

Query: 368 FVGPTIFSGVTREMSVYQEEIFGPVLCVMAAATMDEAIELINANPNGNGTAIFTRSGAAA 427
           FVGPTIFSGVT +M +YQEEIFGPVL ++ A T+++AI L+N+NPNGNGTA+FT+SGAAA
Sbjct: 366 FVGPTIFSGVTTDMRIYQEEIFGPVLVILEAETLEDAIALVNSNPNGNGTAVFTQSGAAA 425

Query: 428 RHFQEEIDVGQVGINVPIPVPVPMFSFTGSRASKLGDLGPYGKQVVQFYTQTKTITERWF 487
           R FQE+IDVGQVGINVPIPVPVP+FSFTGSRASKLGDLGPYGKQVV FYTQTKTIT RWF
Sbjct: 426 RKFQEDIDVGQVGINVPIPVPVPLFSFTGSRASKLGDLGPYGKQVVMFYTQTKTITARWF 485

Query: 488 DENEVGGPVNTTINLK 503
           D+  +G  VNTTI+LK
Sbjct: 486 DDETLGHGVNTTISLK 501


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: 794
Number of extensions: 22
Number of successful extensions: 2
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: 501
Length adjustment: 34
Effective length of query: 469
Effective length of database: 467
Effective search space:   219023
Effective search space used:   219023
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_057507564.1 ABB28_RS04920 (methylmalonate-semialdehyde dehydrogenase (CoA acylating))
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.31980.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.1e-226  737.5   2.6   3.5e-226  737.3   2.6    1.0  1  lcl|NCBI__GCF_001431535.1:WP_057507564.1  ABB28_RS04920 methylmalonate-sem


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001431535.1:WP_057507564.1  ABB28_RS04920 methylmalonate-semialdehyde dehydrogenase (CoA acylating)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  737.3   2.6  3.5e-226  3.5e-226       1     477 []       8     484 ..       8     484 .. 1.00

  Alignments for each domain:
  == domain 1  score: 737.3 bits;  conditional E-value: 3.5e-226
                                 TIGR01722   1 vkhlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllry 69 
                                               +++lidG+f+e+ ++++ +v npat++vla+v++a++ evd ava+a+e+f +w++t++  rar++l+y
  lcl|NCBI__GCF_001431535.1:WP_057507564.1   8 IRLLIDGQFIESSTAHWQDVVNPATQDVLAQVPFATTSEVDDAVAAAKEAFKTWRKTPIGTRARIFLKY 76 
                                               5899***************************************************************** PP

                                 TIGR01722  70 qallkehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplG 138
                                               q+l++e+  e+a+ +saeqGkt+ da+Gdv+rGlevveha ++  l lGe+ ++va+ vd+y++ qplG
  lcl|NCBI__GCF_001431535.1:WP_057507564.1  77 QQLIRENMSELAHTLSAEQGKTVPDAEGDVFRGLEVVEHAAAIGNLQLGELANNVANGVDTYTLMQPLG 145
                                               ********************************************************************* PP

                                 TIGR01722 139 vvaGitpfnfpamiplwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavd 207
                                               v+aGitpfnfpamiplwmfp+aia Gntfvlkpse++p  +++l el +eaG+p+GvlnvvhG++e v+
  lcl|NCBI__GCF_001431535.1:WP_057507564.1 146 VCAGITPFNFPAMIPLWMFPMAIATGNTFVLKPSEQDPMVTMRLVELALEAGIPKGVLNVVHGGEEVVN 214
                                               ********************************************************************* PP

                                 TIGR01722 208 rllehpdvkavsfvGsvavgeyiyetgsahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGq 276
                                                +++hpd+kavsfvGs++vg ++y+++s  gkrvq+++Gaknh+vvlpda+ke++l+a+vgaa+GaaGq
  lcl|NCBI__GCF_001431535.1:WP_057507564.1 215 AICDHPDIKAVSFVGSTRVGTHVYNRASLAGKRVQCMMGAKNHAVVLPDANKEQTLNAMVGAAFGAAGQ 283
                                               ********************************************************************* PP

                                 TIGR01722 277 rcmaisaavlvGaakelveeireraekvrvgagddpgaelGplitkqakervasliasgakeGaevlld 345
                                               rcma s+ vlvG+a+ +v++++ +a+ ++v+ag+ +g+++Gp+i+ +a+erv+ liasg ++Ga + ld
  lcl|NCBI__GCF_001431535.1:WP_057507564.1 284 RCMAASTLVLVGEARSWVPDLVAKAKTLKVSAGSVAGTDVGPVISCSARERVEGLIASGLEQGATLDLD 352
                                               ********************************************************************* PP

                                 TIGR01722 346 GrgykveGyeeGnfvGitllervkpdmkiykeeifGpvlvvleadtleeaiklinespyGnGtaiftsd 414
                                               Gr+ +v+G+e+GnfvG+t++++v +dm+iy+eeifGpvlv+lea+tle+ai+l+n +p GnGta+ft++
  lcl|NCBI__GCF_001431535.1:WP_057507564.1 353 GRNPQVDGFEKGNFVGPTIFSGVTTDMRIYQEEIFGPVLVILEAETLEDAIALVNSNPNGNGTAVFTQS 421
                                               ********************************************************************* PP

                                 TIGR01722 415 GaaarkfqheievGqvGvnvpipvplpffsftGwkdslfGdlhiyGkqGvrfytrlktvtarw 477
                                               Gaaarkfq +i+vGqvG+nvpipvp+p+fsftG+++s  Gdl  yGkq v fyt++kt+tarw
  lcl|NCBI__GCF_001431535.1:WP_057507564.1 422 GAAARKFQEDIDVGQVGINVPIPVPVPLFSFTGSRASKLGDLGPYGKQVVMFYTQTKTITARW 484
                                               *************************************************************** PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (477 nodes)
Target sequences:                          1  (501 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: 10.09
//
[ok]

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

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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 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