Alignments for a candidate for mmsA in Rhodomicrobium vannielii ATCC 17100

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Rhodomicrobium vannielii ATCC 17100

Align Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27) (characterized)
to candidate WP_013420951.1 RVAN_RS17095 CoA-acylating methylmalonate-semialdehyde dehydrogenase

Query= reanno::Caulo:CCNA_01360
         (500 letters)



>NCBI__GCF_000166055.1:WP_013420951.1
          Length = 496

 Score =  644 bits (1661), Expect = 0.0
 Identities = 317/496 (63%), Positives = 381/496 (76%), Gaps = 1/496 (0%)

Query: 4   DIPHFIGGQKVDGASGRFGEVFDPNTGKVQARVALASAGELNTAIANAKVAQAAWAATNP 63
           ++ HF+GG+ + G SGRF +VF+P TGKV+  VALA+  E+  A+ NAK AQ  WAA NP
Sbjct: 2   ELGHFVGGKMIAGQSGRFADVFNPATGKVEKTVALATKAEVRAAVENAKAAQPGWAAVNP 61

Query: 64  QRRARVMFEFKRLLEVHMDELAALLSSEHGKVIADSKGDIQRGLEVIEFACGVPHLLKGE 123
           QRRARV+ EF RLL   MD+LA  LS EHGK   D+KGDI RGLEV EF  G PHLLKGE
Sbjct: 62  QRRARVIMEFVRLLHRDMDKLAEALSREHGKTFPDAKGDIIRGLEVAEFCIGAPHLLKGE 121

Query: 124 YTQGAGPGIDVYSMRQPLGVVAGITPFNFPAMIPMWMFGPAIATGNAFILKPSERDPSVP 183
           +++G GPGID+YS+RQPLGVVAGITPFNFPAMIPMW F PAIA GNAFILKPSER PSVP
Sbjct: 122 FSEGVGPGIDIYSVRQPLGVVAGITPFNFPAMIPMWKFCPAIAAGNAFILKPSERAPSVP 181

Query: 184 VRLAELMIEAGLPPGVLNVVHGDKDCVEAILDHPDIKAVSFVGSSDIAQSVFQRAGAAGK 243
           + LA LM EAGLP G+LNVV+GDK+ V+AILD  DI AV FVGS+ IA+ ++ R  AAGK
Sbjct: 182 LMLAALMQEAGLPDGILNVVNGDKEAVDAILDDTDICAVGFVGSTAIAEYIYTRGCAAGK 241

Query: 244 RVQAMGGAKNHGLVMPDADLDQAVADIIGAAYGSAGERCMALPVVVPVGEKTATALREKL 303
           RVQ  GGAKNH ++ PDADLDQ    +IGA YG+AGERCMA+ V VP+G+ TA  L E+L
Sbjct: 242 RVQCFGGAKNHMVIAPDADLDQVADALIGAGYGAAGERCMAISVAVPIGKDTADRLLERL 301

Query: 304 VAAIGGLRVGVSTDPDAHYGPVVSAAHKARIESYIQMGVDEGAELVVDGRGFSLQGHEEG 363
           +  +  L+VG  T     +GP+V+A  K R+   +  G+ EGA LVVDGRGFSLQG+E+G
Sbjct: 302 IPRVEKLKVGPYTSETVDFGPLVTADAKRRVLGLVDKGIAEGASLVVDGRGFSLQGYEDG 361

Query: 364 FFVGPTLFDHVKPTSRSYHDEIFGPVLQMVRAESLEEGIALASRHQYGNGVAIFTRNGDA 423
           FFVGP LFD+VKP    Y  EIFGPVL +VRA++ EE + L  +H+YGNGVAIFTR+GD 
Sbjct: 362 FFVGPCLFDNVKPDMEIYKAEIFGPVLSIVRADTYEEALDLPMKHEYGNGVAIFTRDGDT 421

Query: 424 AREFADQVEVGMVGINVPIPVPVAYHSFGGWKRSGFGDLNQYGMDGVRFYTRTKTVTQRW 483
           AR+FA +V VGMVGINVPIPVP+A+++FGGWKRSGFGDLNQ+G D  RFYT+TKT+T RW
Sbjct: 422 ARDFASRVNVGMVGINVPIPVPLAHYTFGGWKRSGFGDLNQFGADSFRFYTKTKTITSRW 481

Query: 484 PKGGAVLDQSFVIPTM 499
           P  G     SFVIPTM
Sbjct: 482 P-SGVKEGASFVIPTM 496


Lambda     K      H
   0.320    0.137    0.409 

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: 839
Number of extensions: 26
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: 500
Length of database: 496
Length adjustment: 34
Effective length of query: 466
Effective length of database: 462
Effective search space:   215292
Effective search space used:   215292
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_013420951.1 RVAN_RS17095 (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.1818667.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.9e-196  637.9   0.1   5.6e-196  637.7   0.1    1.0  1  NCBI__GCF_000166055.1:WP_013420951.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000166055.1:WP_013420951.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  637.7   0.1  5.6e-196  5.6e-196       3     477 .]       5     481 ..       3     481 .. 0.99

  Alignments for each domain:
  == domain 1  score: 637.7 bits;  conditional E-value: 5.6e-196
                             TIGR01722   3 hlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryqallke 75 
                                           h+++Gk++ g+s+++ +v npat++v   va a+++ev aav  a+ + + wa  +  +rarv++ +  ll+ 
  NCBI__GCF_000166055.1:WP_013420951.1   5 HFVGGKMIAGQSGRFADVFNPATGKVEKTVALATKAEVRAAVENAKAAQPGWAAVNPQRRARVIMEFVRLLHR 77 
                                           9************************************************************************ PP

                             TIGR01722  76 hrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGvvaGitpfnf 148
                                           + d++a+ +s e+Gkt+ dakGd++rGlev e+  + + ll+Ge +e v   +d+ys+rqplGvvaGitpfnf
  NCBI__GCF_000166055.1:WP_013420951.1  78 DMDKLAEALSREHGKTFPDAKGDIIRGLEVAEFCIGAPHLLKGEFSEGVGPGIDIYSVRQPLGVVAGITPFNF 150
                                           ************************************************************************* PP

                             TIGR01722 149 pamiplwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdrllehpdvkavsfv 221
                                           pamip+w f  aia Gn+f+lkpse+ ps  + la l++eaG+pdG+lnvv Gdkeavd +l+  d+ av fv
  NCBI__GCF_000166055.1:WP_013420951.1 151 PAMIPMWKFCPAIAAGNAFILKPSERAPSVPLMLAALMQEAGLPDGILNVVNGDKEAVDAILDDTDICAVGFV 223
                                           ************************************************************************* PP

                             TIGR01722 222 GsvavgeyiyetgsahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqrcmaisaavlvGa..ake 292
                                           Gs+a++eyiy++g+a gkrvq+++Gaknhmv+ pdad+++++dal+ga +GaaG+rcmais+av +G+  a++
  NCBI__GCF_000166055.1:WP_013420951.1 224 GSTAIAEYIYTRGCAAGKRVQCFGGAKNHMVIAPDADLDQVADALIGAGYGAAGERCMAISVAVPIGKdtADR 296
                                           *******************************************************************73359* PP

                             TIGR01722 293 lveeireraekvrvgagddpgaelGplitkqakervasliasgakeGaevlldGrgykveGyeeGnfvGitll 365
                                           l+e++  r+ek++vg+++  + ++Gpl+t +ak rv  l+++g++eGa++++dGrg+ ++Gye+G fvG++l+
  NCBI__GCF_000166055.1:WP_013420951.1 297 LLERLIPRVEKLKVGPYTSETVDFGPLVTADAKRRVLGLVDKGIAEGASLVVDGRGFSLQGYEDGFFVGPCLF 369
                                           ************************************************************************* PP

                             TIGR01722 366 ervkpdmkiykeeifGpvlvvleadtleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGvnvpipv 438
                                           ++vkpdm+iyk eifGpvl +++adt+eea+ l  +  yGnG aift+dG +ar f  +++vG+vG+nvpipv
  NCBI__GCF_000166055.1:WP_013420951.1 370 DNVKPDMEIYKAEIFGPVLSIVRADTYEEALDLPMKHEYGNGVAIFTRDGDTARDFASRVNVGMVGINVPIPV 442
                                           ************************************************************************* PP

                             TIGR01722 439 plpffsftGwkdslfGdlhiyGkqGvrfytrlktvtarw 477
                                           pl+ ++f+Gwk s fGdl+ +G +  rfyt++kt+t+rw
  NCBI__GCF_000166055.1:WP_013420951.1 443 PLAHYTFGGWKRSGFGDLNQFGADSFRFYTKTKTITSRW 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 13.57
//
[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