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 malonate-semialdehyde dehydrogenase (EC 1.2.1.15); malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_099020112.1 CCS90_RS13530 CoA-acylating methylmalonate-semialdehyde dehydrogenase

Query= BRENDA::A0A081YAY7
         (498 letters)



>NCBI__GCF_002591915.1:WP_099020112.1
          Length = 498

 Score =  590 bits (1522), Expect = e-173
 Identities = 289/497 (58%), Positives = 367/497 (73%), Gaps = 2/497 (0%)

Query: 1   MTLIKHLIGGELIA-DTGRTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNT 59
           M  I+H+I G+  +  +G+T  VFNP+ G+   ++ L   + +  A+ ++ AAF  W  T
Sbjct: 1   MATIQHIINGQRTSGSSGQTQAVFNPANGQQSGELVLGGSDEVNTAVKSSLAAFELWSAT 60

Query: 60  PPAKRAQVLFRFKQLLEANEERIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEILK 119
            PAKRA V+F  +QLL    + +   IS+EHGKT +DA GE+ R +E VEYA    E LK
Sbjct: 61  APAKRAAVMFNMRQLLMDRADEVALTISKEHGKTHDDALGEVTRALEVVEYACGITEKLK 120

Query: 120 GEYSRNVGPNIDAWSDFQPIGVVAGITPFNFPAMVPLWMYPLAIACGNTFILKPSERDPS 179
           G+++ NVGP ID  S+ QP+GVVAGITPFNFPAMVPLWM P+A+A GN+FILKPSERDPS
Sbjct: 121 GDFNANVGPGIDTHSERQPLGVVAGITPFNFPAMVPLWMIPMALATGNSFILKPSERDPS 180

Query: 180 STLLIAELFHEAGLPKGVLNVVHGDKGAVDALIEAPEVKALSFVGSTPIAEYIYSEGTKR 239
           S  L+ +LF EAGLP GVLNVVHG K AVDA+++ P++KA+SFVGSTPIAEY+Y+ G   
Sbjct: 181 SANLVHDLFIEAGLPAGVLNVVHGGKEAVDAILDHPDIKAVSFVGSTPIAEYVYTRGCAS 240

Query: 240 GKRVQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADALVQ 299
           GKRVQALGGAKNH ++MPDADLD A  ALMGA +GS GERCMAIS+AV VGD+ AD L+ 
Sbjct: 241 GKRVQALGGAKNHMIIMPDADLDQAADALMGAGFGSAGERCMAISMAVPVGDETADRLIA 300

Query: 300 KLVPQIKGLKIGAGTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAGHE 359
           KL PQ++ L IG     G +MGP++T  A+ ++ G I  G A+GA +VVDGR ++V G+E
Sbjct: 301 KLKPQVEALNIGPYNQEGAEMGPVITAEAKSRIEGMITQGEAEGAHVVVDGRNHQVDGYE 360

Query: 360 NGFFLGGTLFDRVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRDG 419
            GF++G TL D V  EM++YK+EIFGPVL ++R  + +EA+ LIN HEYGNGT IFTRDG
Sbjct: 361 QGFWVGATLLDHVKAEMSVYKQEIFGPVLSVLRAKNYDEAVALINSHEYGNGTAIFTRDG 420

Query: 420 EAARLFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYTKRKAITQ 479
           +AAR F  +I+VGMVG+NVP+PVPVAYHSFGGWKRS+FG    YGP+ V FYTK K +T 
Sbjct: 421 DAARNFASKIQVGMVGINVPIPVPVAYHSFGGWKRSIFGAHGIYGPEAVHFYTKLKTVTS 480

Query: 480 RWPQRKSHEAAQFAFPS 496
           RWP       AQF FPS
Sbjct: 481 RWP-TGIRSGAQFNFPS 496


Lambda     K      H
   0.319    0.137    0.411 

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: 736
Number of extensions: 28
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: 498
Length adjustment: 34
Effective length of query: 464
Effective length of database: 464
Effective search space:   215296
Effective search space used:   215296
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_099020112.1 CCS90_RS13530 (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.1359419.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.2e-208  679.6   2.0   1.4e-208  679.3   2.0    1.0  1  NCBI__GCF_002591915.1:WP_099020112.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002591915.1:WP_099020112.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  679.3   2.0  1.4e-208  1.4e-208       1     477 []       4     482 ..       4     482 .. 0.99

  Alignments for each domain:
  == domain 1  score: 679.3 bits;  conditional E-value: 1.4e-208
                             TIGR01722   1 vkhlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryqall 73 
                                           ++h+i+G+   g s++   v npa+++  +++     +ev++av s+  +f  w+ t+ a+ra v++  ++ll
  NCBI__GCF_002591915.1:WP_099020112.1   4 IQHIINGQRTSGSSGQTQAVFNPANGQQSGELVLGGSDEVNTAVKSSLAAFELWSATAPAKRAAVMFNMRQLL 76 
                                           589********************************************************************** PP

                             TIGR01722  74 kehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGvvaGitpf 146
                                            ++ de+a  is e+Gkt++da G+v r levve+ac++t +l+G+   +v   +d++s rqplGvvaGitpf
  NCBI__GCF_002591915.1:WP_099020112.1  77 MDRADEVALTISKEHGKTHDDALGEVTRALEVVEYACGITEKLKGDFNANVGPGIDTHSERQPLGVVAGITPF 149
                                           ************************************************************************* PP

                             TIGR01722 147 nfpamiplwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdrllehpdvkavs 219
                                           nfpam+plwm p+a+a Gn+f+lkpse++ps+a  + +l+ eaG+p GvlnvvhG+keavd +l+hpd+kavs
  NCBI__GCF_002591915.1:WP_099020112.1 150 NFPAMVPLWMIPMALATGNSFILKPSERDPSSANLVHDLFIEAGLPAGVLNVVHGGKEAVDAILDHPDIKAVS 222
                                           ************************************************************************* PP

                             TIGR01722 220 fvGsvavgeyiyetgsahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqrcmaisaavlvGaa.. 290
                                           fvGs++++ey+y++g+a gkrvqal+Gaknhm+++pdad+++a+dal+ga +G+aG+rcmais+av vG+   
  NCBI__GCF_002591915.1:WP_099020112.1 223 FVGSTPIAEYVYTRGCASGKRVQALGGAKNHMIIMPDADLDQAADALMGAGFGSAGERCMAISMAVPVGDEta 295
                                           *********************************************************************7444 PP

                             TIGR01722 291 kelveeireraekvrvgagddpgaelGplitkqakervasliasgakeGaevlldGrgykveGyeeGnfvGit 363
                                           ++l+ +++ ++e +++g++++ gae+Gp+it +ak r++ +i++g +eGa+v++dGr+ +v+Gye+G +vG t
  NCBI__GCF_002591915.1:WP_099020112.1 296 DRLIAKLKPQVEALNIGPYNQEGAEMGPVITAEAKSRIEGMITQGEAEGAHVVVDGRNHQVDGYEQGFWVGAT 368
                                           9************************************************************************ PP

                             TIGR01722 364 llervkpdmkiykeeifGpvlvvleadtleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGvnvpi 436
                                           ll++vk++m++yk+eifGpvl vl+a  ++ea++lin   yGnGtaift+dG aar+f  +i+vG+vG+nvpi
  NCBI__GCF_002591915.1:WP_099020112.1 369 LLDHVKAEMSVYKQEIFGPVLSVLRAKNYDEAVALINSHEYGNGTAIFTRDGDAARNFASKIQVGMVGINVPI 441
                                           ************************************************************************* PP

                             TIGR01722 437 pvplpffsftGwkdslfGdlhiyGkqGvrfytrlktvtarw 477
                                           pvp++++sf+Gwk s+fG + iyG + v+fyt+lktvt+rw
  NCBI__GCF_002591915.1:WP_099020112.1 442 PVPVAYHSFGGWKRSIFGAHGIYGPEAVHFYTKLKTVTSRW 482
                                           ***************************************** 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 15.05
//
[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