Alignments for a candidate for mmsA in Azospirillum sp. B510

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Azospirillum sp. B510

Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_012976631.1 AZL_RS21870 CoA-acylating methylmalonate-semialdehyde dehydrogenase

Query= BRENDA::G5CZI2
         (498 letters)



>NCBI__GCF_000010725.1:WP_012976631.1
          Length = 500

 Score =  633 bits (1633), Expect = 0.0
 Identities = 306/497 (61%), Positives = 388/497 (78%), Gaps = 3/497 (0%)

Query: 4   IGHLINGQLVTENTRSQNVFNPATGEIGKQLDLASTKTVEQAISAAQHAFPTWRNTPPLK 63
           + H I G LV     S +VFNPATG +  ++ LA+   V++A++AA+ A+P W    PL+
Sbjct: 5   VQHFIGGALVDGAGGSGDVFNPATGRVVARVPLATAAEVDKAVAAARAAWPAWAAATPLR 64

Query: 64  RARVMFRFKELLEQHADEICRLIGEEHGKIAHDAMGELQRGIENVEYACGAPELLKGEHS 123
           RARVMF FK+LLEQ+AD +  LI  EHGKI  DA+GE+ RG+E VE+ACG P LLKGE +
Sbjct: 65  RARVMFAFKQLLEQNADALANLITAEHGKIHSDALGEVTRGLEVVEFACGGPHLLKGEVA 124

Query: 124 RNVGPGIDSWSEFQPMGVVAGITPFNFPVMVPLWMFPMAIVCGNCFVLKPSERDPSSTLY 183
            NVG G+DS S  QP+GVVAGITPFNFP MVP+WMFP+AI CGN F+LKPSER PS+ L+
Sbjct: 125 ENVGTGVDSHSLRQPLGVVAGITPFNFPAMVPMWMFPVAIACGNSFILKPSERVPSAALF 184

Query: 184 IAQLLQEAGLPDGVMNVVNGDKEAVDALLHDDRVKAVSFVGSTPIAEYIYRTASANGKRC 243
           +A+LL++AGLPDGV NVV+GDK AVDALL    VKAVSFVGSTP+A YIY T +ANGKR 
Sbjct: 185 LARLLKQAGLPDGVFNVVHGDKAAVDALLSHPDVKAVSFVGSTPVARYIYATGAANGKRV 244

Query: 244 QALGGAKNHAIVMPDADMDNAVNQLLGAAFGSSGERCMALSVAVAVGDAAGDALVSKMTQ 303
           QALGGAKNH ++MPDAD+D AV+ L+GAA+GS+GERCMA+SVAV V DA  DALV+++ +
Sbjct: 245 QALGGAKNHMVIMPDADLDQAVDALMGAAYGSAGERCMAISVAVPVTDAVADALVARLAE 304

Query: 304 AMQKLKVGPSTDSGNDFGPVITRQHQEKVIGYINSAEQQGATIVVDGRQPKV--PNHENG 361
            ++ LK+GP TD   + GP++TR H+++V GYI+    +GAT+VVDGR+  V  P+  +G
Sbjct: 305 RVRALKIGPGTDPNAEMGPLVTRAHRDRVRGYIDLGVAEGATLVVDGREASVSDPDCADG 364

Query: 362 FFVGGTLIDHVTPEMTSYQEEIFGPVLQVVRVATMQDAMDLIDAHEYGNGTCIFTRDGEA 421
           +F+GG L DHVTPEM  Y+EEIFGPVL VVRV   + A  LI+AHE+GNGT IFTRDG+ 
Sbjct: 365 YFLGGNLFDHVTPEMRIYKEEIFGPVLAVVRVPDYRTAATLINAHEFGNGTAIFTRDGDT 424

Query: 422 ARYFSDNIQVGMVGINIPLPVPVAYHSFGGWKRSLFGDLHAYGPDAVRFYTKRKTVTQRW 481
           AR F   I+VGMVG+N+P+PVP+A+HSFGGWK SLFGD H +GP+ VRFYT+ KT+T RW
Sbjct: 425 ARAFGAEIEVGMVGVNVPIPVPMAFHSFGGWKGSLFGDHHMHGPEGVRFYTRLKTITSRW 484

Query: 482 PSAGVREGAEFSMPTMK 498
           P+ G+R GA+F MPTMK
Sbjct: 485 PT-GIRAGADFVMPTMK 500


Lambda     K      H
   0.319    0.135    0.405 

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: 789
Number of extensions: 33
Number of successful extensions: 3
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: 498
Length of database: 500
Length adjustment: 34
Effective length of query: 464
Effective length of database: 466
Effective search space:   216224
Effective search space used:   216224
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 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate WP_012976631.1 AZL_RS21870 (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.2874015.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.7e-219  715.3   1.2   1.9e-219  715.1   1.2    1.0  1  NCBI__GCF_000010725.1:WP_012976631.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000010725.1:WP_012976631.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  715.1   1.2  1.9e-219  1.9e-219       1     477 []       5     484 ..       5     484 .. 0.99

  Alignments for each domain:
  == domain 1  score: 715.1 bits;  conditional E-value: 1.9e-219
                             TIGR01722   1 vkhlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryqall 73 
                                           v+h+i+G++v+g+++  ++v npat+ v+a+v+ a+a+evd+ava+ar +++awa ++ ++rarv++ +++ll
  NCBI__GCF_000010725.1:WP_012976631.1   5 VQHFIGGALVDGAGG-SGDVFNPATGRVVARVPLATAAEVDKAVAAARAAWPAWAAATPLRRARVMFAFKQLL 76 
                                           89**********987.59******************************************************* PP

                             TIGR01722  74 kehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGvvaGitpf 146
                                           +++ d +a+li+ae+Gk+++da G+v rGlevve+ac+ + ll+Ge+ e+v + vd +s+rqplGvvaGitpf
  NCBI__GCF_000010725.1:WP_012976631.1  77 EQNADALANLITAEHGKIHSDALGEVTRGLEVVEFACGGPHLLKGEVAENVGTGVDSHSLRQPLGVVAGITPF 149
                                           ************************************************************************* PP

                             TIGR01722 147 nfpamiplwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdrllehpdvkavs 219
                                           nfpam+p+wmfp+aiacGn+f+lkpse+vpsaa+ la+ll++aG+pdGv+nvvhGdk avd ll hpdvkavs
  NCBI__GCF_000010725.1:WP_012976631.1 150 NFPAMVPMWMFPVAIACGNSFILKPSERVPSAALFLARLLKQAGLPDGVFNVVHGDKAAVDALLSHPDVKAVS 222
                                           ************************************************************************* PP

                             TIGR01722 220 fvGsvavgeyiyetgsahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqrcmaisaavlvGaa.. 290
                                           fvGs++v++yiy tg+a+gkrvqal+Gaknhmv++pdad+++a+dal+gaa+G+aG+rcmais+av v +a  
  NCBI__GCF_000010725.1:WP_012976631.1 223 FVGSTPVARYIYATGAANGKRVQALGGAKNHMVIMPDADLDQAVDALMGAAYGSAGERCMAISVAVPVTDAva 295
                                           *******************************************************************998767 PP

                             TIGR01722 291 kelveeireraekvrvgagddpgaelGplitkqakervasliasgakeGaevlldGrgykveG..yeeGnfvG 361
                                           + lv ++ er++ +++g+g+dp+ae+Gpl+t+++++rv  +i+ g++eGa +++dGr   v      +G f+G
  NCBI__GCF_000010725.1:WP_012976631.1 296 DALVARLAERVRALKIGPGTDPNAEMGPLVTRAHRDRVRGYIDLGVAEGATLVVDGREASVSDpdCADGYFLG 368
                                           99********************************************************999862267****** PP

                             TIGR01722 362 itllervkpdmkiykeeifGpvlvvleadtleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGvnv 434
                                             l+++v p+m+iykeeifGpvl+v+++  +  a  lin+  +GnGtaift+dG +ar f  eievG+vGvnv
  NCBI__GCF_000010725.1:WP_012976631.1 369 GNLFDHVTPEMRIYKEEIFGPVLAVVRVPDYRTAATLINAHEFGNGTAIFTRDGDTARAFGAEIEVGMVGVNV 441
                                           ************************************************************************* PP

                             TIGR01722 435 pipvplpffsftGwkdslfGdlhiyGkqGvrfytrlktvtarw 477
                                           pipvp++f+sf+Gwk+slfGd+h++G +Gvrfytrlkt+t+rw
  NCBI__GCF_000010725.1:WP_012976631.1 442 PIPVPMAFHSFGGWKGSLFGDHHMHGPEGVRFYTRLKTITSRW 484
                                           ******************************************* PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (477 nodes)
Target sequences:                          1  (500 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: 00:00:00.00
# Mc/sec: 30.76
//
[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