Alignments for a candidate for mmsA in Marinicella litoralis KMM 3900

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Marinicella litoralis KMM 3900

Align Methylmalonate-semialdehyde dehydrogenase [acylating]; MMSDH; EC 1.2.1.27 (characterized)
to candidate WP_099020246.1 CCS90_RS14240 CoA-acylating methylmalonate-semialdehyde dehydrogenase

Query= SwissProt::P28810
         (497 letters)



>NCBI__GCF_002591915.1:WP_099020246.1
          Length = 498

 Score =  684 bits (1765), Expect = 0.0
 Identities = 320/485 (65%), Positives = 398/485 (82%)

Query: 1   MSVPVRHLIAGAFVEGLGAQRIPVSNPLDNSTLAEIACASAEQVEQAVASARETFASWKE 60
           M+  V   I G  V    A  + V++P     + ++  A+  ++E+A+ASA++ F +WK+
Sbjct: 1   MTRKVSMFIDGQSVISESADWMDVTDPATQEAICQVPMATEAEMEKAIASAKKAFETWKD 60

Query: 61  TPVSERARVMLRYQALLKEHHDELAKIVSSELGKTFEDAKGDVWRGIEVVEHACNVPSLL 120
            PV++RAR+ML YQ LLKEHHDELA+I++ E GK FEDAKGDVWRGIEV EHA N+PS++
Sbjct: 61  VPVTKRARMMLNYQHLLKEHHDELAEILAEETGKNFEDAKGDVWRGIEVAEHAANIPSMM 120

Query: 121 MGETVENVARNIDTYSITQPLGVCVGITPFNFPAMIPLWMFPLAIACGNAFILKPSEQVP 180
           MGETVENVA  +DTYS+ QPLGVC GITPFNFPAMIPLWMFP+A+ CGN F+LKPSEQ P
Sbjct: 121 MGETVENVASQVDTYSLIQPLGVCAGITPFNFPAMIPLWMFPMAVVCGNTFVLKPSEQDP 180

Query: 181 LTSVRLAELFLEAGAPKGVLQVVHGGKEQVDQLLKHPQVKAVSFVGSVAVGQYVYHTGTA 240
            T +RLAELF EAG P+ VLQVVHGGK+QV+Q+L H  ++A+SFVGSV VG+++Y TGT 
Sbjct: 181 NTPMRLAELFYEAGFPRDVLQVVHGGKDQVNQILHHEDIQAISFVGSVPVGEHIYKTGTD 240

Query: 241 HNKRVQSFAGAKNHMVIMPDADKAQVISNLVGASVGAAGQRCMAISVAVLVGAAREWIPE 300
           + KRVQ+FAGAKNHMV+MPDA+K QVI+N+ G+S GAAGQRCMAISVAVLVG A++W+ E
Sbjct: 241 NLKRVQAFAGAKNHMVVMPDANKNQVINNIAGSSCGAAGQRCMAISVAVLVGEAKDWLEE 300

Query: 301 IRDALAKVRPGPWDDSGASYGPVINPQAKARIERLIGQGVEEGAQLLLDGRGYKVEGYPD 360
           I+  +++++PG W D  + YGP+I+PQAKA++E LI  GV+EGA L+LDGR  KVEGYPD
Sbjct: 301 IKGKMSEMQPGYWKDPKSFYGPLISPQAKAKVESLIQSGVDEGADLMLDGRNLKVEGYPD 360

Query: 361 GNWVGPTLFAGVRPDMAIYREEVFGPVLCLAEVDSLEQAIRLINESPYGNGTSIFTSSGA 420
           GNW+GP+LF+ V  +M IY EE+FGPVLC+   D+LE+AI LIN +PYGNGTS+FTSSGA
Sbjct: 361 GNWLGPSLFSNVTTEMRIYNEEIFGPVLCVMTADTLEEAIELINNNPYGNGTSLFTSSGA 420

Query: 421 AARTFQHHIEVGQVGINIPIPVPLPFFSFTGWKGSFYGDLHAYGKQGVRFYTETKTVTAR 480
           AAR FQH I+VGQVGINIPIPVPLPFFSFTGW+ SFYGD HAYGKQ VRFYTETKT+TAR
Sbjct: 421 AARKFQHEIKVGQVGINIPIPVPLPFFSFTGWRKSFYGDQHAYGKQAVRFYTETKTITAR 480

Query: 481 WFDSD 485
           WF+SD
Sbjct: 481 WFESD 485


Lambda     K      H
   0.319    0.135    0.406 

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: 821
Number of extensions: 31
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: 497
Length of database: 498
Length adjustment: 34
Effective length of query: 463
Effective length of database: 464
Effective search space:   214832
Effective search space used:   214832
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 (21.8 bits)
S2: 52 (24.6 bits)

Align candidate WP_099020246.1 CCS90_RS14240 (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.3727880.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.3e-243  794.8   0.1   1.5e-243  794.6   0.1    1.0  1  NCBI__GCF_002591915.1:WP_099020246.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002591915.1:WP_099020246.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  794.6   0.1  1.5e-243  1.5e-243       1     477 []       5     481 ..       5     481 .. 1.00

  Alignments for each domain:
  == domain 1  score: 794.6 bits;  conditional E-value: 1.5e-243
                             TIGR01722   1 vkhlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryqall 73 
                                           v ++idG+ v ++s+ +++v++pat+e +++v++a+ +e+++a+asa+++f +w++ +v++rar++l yq ll
  NCBI__GCF_002591915.1:WP_099020246.1   5 VSMFIDGQSVISESADWMDVTDPATQEAICQVPMATEAEMEKAIASAKKAFETWKDVPVTKRARMMLNYQHLL 77 
                                           678********************************************************************** PP

                             TIGR01722  74 kehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGvvaGitpf 146
                                           keh+de+a++++ e Gk +edakGdv+rG+ev eha +++s+++Getve+va +vd+ys+ qplGv+aGitpf
  NCBI__GCF_002591915.1:WP_099020246.1  78 KEHHDELAEILAEETGKNFEDAKGDVWRGIEVAEHAANIPSMMMGETVENVASQVDTYSLIQPLGVCAGITPF 150
                                           ************************************************************************* PP

                             TIGR01722 147 nfpamiplwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdrllehpdvkavs 219
                                           nfpamiplwmfp+a++cGntfvlkpse++p++ ++lael+ eaG p  vl+vvhG+k++v+++l+h d++a+s
  NCBI__GCF_002591915.1:WP_099020246.1 151 NFPAMIPLWMFPMAVVCGNTFVLKPSEQDPNTPMRLAELFYEAGFPRDVLQVVHGGKDQVNQILHHEDIQAIS 223
                                           ************************************************************************* PP

                             TIGR01722 220 fvGsvavgeyiyetgsahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqrcmaisaavlvGaake 292
                                           fvGsv+vge+iy+tg+ + krvqa+aGaknhmvv+pda+k+++++++ g++ GaaGqrcmais+avlvG+ak+
  NCBI__GCF_002591915.1:WP_099020246.1 224 FVGSVPVGEHIYKTGTDNLKRVQAFAGAKNHMVVMPDANKNQVINNIAGSSCGAAGQRCMAISVAVLVGEAKD 296
                                           ************************************************************************* PP

                             TIGR01722 293 lveeireraekvrvgagddpgaelGplitkqakervasliasgakeGaevlldGrgykveGyeeGnfvGitll 365
                                           ++eei+ ++  +++g ++dp + +Gpli++qak++v+sli+sg++eGa+++ldGr++kveGy++Gn++G++l+
  NCBI__GCF_002591915.1:WP_099020246.1 297 WLEEIKGKMSEMQPGYWKDPKSFYGPLISPQAKAKVESLIQSGVDEGADLMLDGRNLKVEGYPDGNWLGPSLF 369
                                           ************************************************************************* PP

                             TIGR01722 366 ervkpdmkiykeeifGpvlvvleadtleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGvnvpipv 438
                                           ++v ++m+iy+eeifGpvl+v+ adtleeai+lin++pyGnGt++fts+Gaaarkfqhei+vGqvG+n+pipv
  NCBI__GCF_002591915.1:WP_099020246.1 370 SNVTTEMRIYNEEIFGPVLCVMTADTLEEAIELINNNPYGNGTSLFTSSGAAARKFQHEIKVGQVGINIPIPV 442
                                           ************************************************************************* PP

                             TIGR01722 439 plpffsftGwkdslfGdlhiyGkqGvrfytrlktvtarw 477
                                           plpffsftGw++s++Gd+h+yGkq vrfyt++kt+tarw
  NCBI__GCF_002591915.1:WP_099020246.1 443 PLPFFSFTGWRKSFYGDQHAYGKQAVRFYTETKTITARW 481
                                           *************************************** PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (477 nodes)
Target sequences:                          1  (498 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: 35.65
//
[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 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