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 (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_090275928.1 BLU11_RS18585 CoA-acylating methylmalonate-semialdehyde dehydrogenase

Query= BRENDA::G5CZI2
         (498 letters)



>NCBI__GCF_900105005.1:WP_090275928.1
          Length = 496

 Score =  832 bits (2149), Expect = 0.0
 Identities = 402/496 (81%), Positives = 451/496 (90%)

Query: 1   MTTIGHLINGQLVTENTRSQNVFNPATGEIGKQLDLASTKTVEQAISAAQHAFPTWRNTP 60
           M TIGHLING + T+++R+Q+VFNP+TGE+ K+L +AS  TVE AI+AAQ A+P WRNTP
Sbjct: 1   MKTIGHLINGTIDTQSSRTQDVFNPSTGEVSKKLAVASKPTVEAAIAAAQAAYPAWRNTP 60

Query: 61  PLKRARVMFRFKELLEQHADEICRLIGEEHGKIAHDAMGELQRGIENVEYACGAPELLKG 120
           PLKRA+VMFRFKELLE++ADEICRLIGEEHGKIAHDAMGELQRGIENVEYACGAPELLKG
Sbjct: 61  PLKRAKVMFRFKELLERNADEICRLIGEEHGKIAHDAMGELQRGIENVEYACGAPELLKG 120

Query: 121 EHSRNVGPGIDSWSEFQPMGVVAGITPFNFPVMVPLWMFPMAIVCGNCFVLKPSERDPSS 180
           E S+N GP IDSWSEFQP+GVVAGITPFNFP MVPLWM+PMAIVCGN FVLKPSER+PS+
Sbjct: 121 EFSKNAGPAIDSWSEFQPLGVVAGITPFNFPAMVPLWMYPMAIVCGNTFVLKPSERNPSA 180

Query: 181 TLYIAQLLQEAGLPDGVMNVVNGDKEAVDALLHDDRVKAVSFVGSTPIAEYIYRTASANG 240
            L+IA+LL EAGLP GV+NVVNGDKEAVD LL D RV+AVSFVGSTPIAEYIY TASA+G
Sbjct: 181 VLFIAELLHEAGLPPGVLNVVNGDKEAVDVLLSDARVQAVSFVGSTPIAEYIYTTASAHG 240

Query: 241 KRCQALGGAKNHAIVMPDADMDNAVNQLLGAAFGSSGERCMALSVAVAVGDAAGDALVSK 300
           KRCQALGGAKNHAIVMPDADMDNAV+ L+GAAFGSSGERCMALSVAVAVGD A D+L+SK
Sbjct: 241 KRCQALGGAKNHAIVMPDADMDNAVSALVGAAFGSSGERCMALSVAVAVGDEAADSLISK 300

Query: 301 MTQAMQKLKVGPSTDSGNDFGPVITRQHQEKVIGYINSAEQQGATIVVDGRQPKVPNHEN 360
           MT+ M+ LKVG  +D  NDFGP+ITR HQEKV GYI+SAEQQGAT+VVDGRQP V  ++ 
Sbjct: 301 MTEQMKSLKVGAFSDKSNDFGPLITRAHQEKVTGYISSAEQQGATLVVDGRQPAVAGYDK 360

Query: 361 GFFVGGTLIDHVTPEMTSYQEEIFGPVLQVVRVATMQDAMDLIDAHEYGNGTCIFTRDGE 420
           GF+VGGTLID+VT EMT Y+EEIFGPVL V+RV +M++AM LI+ HEYGNGTCIFTRDGE
Sbjct: 361 GFYVGGTLIDNVTAEMTCYKEEIFGPVLLVMRVNSMEEAMQLINDHEYGNGTCIFTRDGE 420

Query: 421 AARYFSDNIQVGMVGINIPLPVPVAYHSFGGWKRSLFGDLHAYGPDAVRFYTKRKTVTQR 480
           AARYFSDNI VGMVGIN+PLPVPVAYHSFGGWKRSLFGDLHAYGPDAVRFYTKRKT+TQR
Sbjct: 421 AARYFSDNIMVGMVGINVPLPVPVAYHSFGGWKRSLFGDLHAYGPDAVRFYTKRKTITQR 480

Query: 481 WPSAGVREGAEFSMPT 496
           WPSAGVREGA+FS P+
Sbjct: 481 WPSAGVREGAQFSFPS 496


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: 862
Number of extensions: 25
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: 498
Length of database: 496
Length adjustment: 34
Effective length of query: 464
Effective length of database: 462
Effective search space:   214368
Effective search space used:   214368
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_090275928.1 BLU11_RS18585 (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.1991773.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.5e-208  679.2   0.3   1.7e-208  679.0   0.3    1.0  1  NCBI__GCF_900105005.1:WP_090275928.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900105005.1:WP_090275928.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  679.0   0.3  1.7e-208  1.7e-208       3     477 .]       6     481 ..       4     481 .. 0.99

  Alignments for each domain:
  == domain 1  score: 679.0 bits;  conditional E-value: 1.7e-208
                             TIGR01722   3 hlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryqallke 75 
                                           hli+G +++++s++  +v np t+ev  k+a+as+  v+aa+a+a+ +++aw++t+ ++ra+v++r+++ll+ 
  NCBI__GCF_900105005.1:WP_090275928.1   6 HLING-TIDTQSSRTQDVFNPSTGEVSKKLAVASKPTVEAAIAAAQAAYPAWRNTPPLKRAKVMFRFKELLER 77 
                                           88888.6899*************************************************************** PP

                             TIGR01722  76 hrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGvvaGitpfnf 148
                                           + dei +li  e+Gk+ +da G++ rG+e ve+ac+ + ll+Ge +++    +d +s  qplGvvaGitpfnf
  NCBI__GCF_900105005.1:WP_090275928.1  78 NADEICRLIGEEHGKIAHDAMGELQRGIENVEYACGAPELLKGEFSKNAGPAIDSWSEFQPLGVVAGITPFNF 150
                                           ************************************************************************* PP

                             TIGR01722 149 pamiplwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdrllehpdvkavsfv 221
                                           pam+plwm+p+ai+cGntfvlkpse++psa + +aell+eaG+p Gvlnvv Gdkeavd ll    v+avsfv
  NCBI__GCF_900105005.1:WP_090275928.1 151 PAMVPLWMYPMAIVCGNTFVLKPSERNPSAVLFIAELLHEAGLPPGVLNVVNGDKEAVDVLLSDARVQAVSFV 223
                                           ************************************************************************* PP

                             TIGR01722 222 GsvavgeyiyetgsahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqrcmaisaavlvG..aake 292
                                           Gs++++eyiy+t+sahgkr qal+Gaknh++v+pdad ++a++alvgaa+G++G+rcma+s+av+vG  aa+ 
  NCBI__GCF_900105005.1:WP_090275928.1 224 GSTPIAEYIYTTASAHGKRCQALGGAKNHAIVMPDADMDNAVSALVGAAFGSSGERCMALSVAVAVGdeAADS 296
                                           *******************************************************************43459* PP

                             TIGR01722 293 lveeireraekvrvgagddpgaelGplitkqakervasliasgakeGaevlldGrgykveGyeeGnfvGitll 365
                                           l+ ++ e+++ ++vga +d + ++Gplit++++e+v+ +i+s+ ++Ga +++dGr   v Gy++G +vG tl+
  NCBI__GCF_900105005.1:WP_090275928.1 297 LISKMTEQMKSLKVGAFSDKSNDFGPLITRAHQEKVTGYISSAEQQGATLVVDGRQPAVAGYDKGFYVGGTLI 369
                                           ************************************************************************* PP

                             TIGR01722 366 ervkpdmkiykeeifGpvlvvleadtleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGvnvpipv 438
                                           ++v ++m++ykeeifGpvl v++++++eea++lin+  yGnGt+ift+dG aar f+ +i vG+vG+nvp+pv
  NCBI__GCF_900105005.1:WP_090275928.1 370 DNVTAEMTCYKEEIFGPVLLVMRVNSMEEAMQLINDHEYGNGTCIFTRDGEAARYFSDNIMVGMVGINVPLPV 442
                                           ************************************************************************* PP

                             TIGR01722 439 plpffsftGwkdslfGdlhiyGkqGvrfytrlktvtarw 477
                                           p++++sf+Gwk slfGdlh+yG + vrfyt+ kt+t rw
  NCBI__GCF_900105005.1:WP_090275928.1 443 PVAYHSFGGWKRSLFGDLHAYGPDAVRFYTKRKTITQRW 481
                                           *************************************** PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (477 nodes)
Target sequences:                          1  (496 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: 00:00:00.01
# Mc/sec: 21.23
//
[ok]

This GapMind analysis is from Sep 24 2021. 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