GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mmsA in Marinobacter adhaerens HP15

Align Methylmalonate-semialdehyde dehydrogenase [acylating]; MMSDH; EC 1.2.1.27 (characterized)
to candidate GFF964 HP15_943 aldehyde dehydrogenase family protein

Query= SwissProt::P28810
         (497 letters)



>lcl|FitnessBrowser__Marino:GFF964 HP15_943 aldehyde dehydrogenase
           family protein
          Length = 505

 Score =  196 bits (499), Expect = 1e-54
 Identities = 153/484 (31%), Positives = 232/484 (47%), Gaps = 27/484 (5%)

Query: 6   RHLIAGAFVEGLGAQRIPVSNPLDNSTLAEIACASAEQVEQAVASARETFAS--WKETPV 63
           R  + G +      +     +P+D   LA IA       +QAV +AR  F +  W +   
Sbjct: 28  RAYLNGTYQWAANGEAFTSVSPIDGRELASIASCDQSDADQAVMAARAAFEAGIWSQLAP 87

Query: 64  SERARVMLRYQALLKEHHDELAKIVSSELGKTFEDAKG-DVWRGIEVVEHACNVPSLLMG 122
           ++R  V+LR+  L++ H DELA + + ++GK    A   DV      +         + G
Sbjct: 88  AKRKAVLLRFAELIEAHGDELALLETLDMGKPINHASNVDVPATARAIRWTAEAIDKVYG 147

Query: 123 ETVENVARNIDTYSITQPLGVCVGITPFNFPAMIPLWMFPLAIACGNAFILKPSEQVPLT 182
           E        I   S  +P+GV   I P+NFP ++  W    A+A GN+ ILKPSE+ PL+
Sbjct: 148 ELAPTPHNQIGMIS-REPMGVVAAIVPWNFPMIMAAWKIAPALATGNSVILKPSEKSPLS 206

Query: 183 SVRLAELFLEAGAPKGVLQVVHGGKEQVDQLLK-HPQVKAVSFVGSVAVG-QYVYHTGTA 240
           ++RLA L  EAG P GV  V+ G    V + L  H  V  + F GS  V  Q + + G +
Sbjct: 207 AIRLAALAGEAGVPAGVFNVLPGYGHTVGKALALHMDVDCLVFTGSTNVAKQLMIYAGQS 266

Query: 241 HNKRVQSFAGAKNHMVIMPDA-DKAQVISNLVGASVGAAGQRCMAISVAVLVGAAR-EWI 298
           + KRV   AG K+  ++  DA D  +  +    A     G+ C A S  ++  + R E++
Sbjct: 267 NMKRVWLEAGGKSPNIVFADAPDLKKAAAEAASAIAFNQGEVCTAGSRLLVENSIRAEFV 326

Query: 299 PEIRDALAKVRPGPWDDSGASYGPVINPQAKARIERLIGQGVEEGAQLLLDGRGYKVEGY 358
             I +AL   RPG   D   + G +++     RI   IG G  EGA+L+  G+  ++   
Sbjct: 327 RLICEALKTWRPGHPLDPATTCGAIVDQAQLDRIIDYIGIGQSEGARLVEGGQ--RILEN 384

Query: 359 PDGNWVGPTLFAGVRPDMAIYREEVFGPVLCLAEVDSLEQAIRLINESPYGNGTSIFTSS 418
             G +V PT+F GV   M I  EE+FGPVL +   D+ ++A+ + N+S YG   +++TS+
Sbjct: 385 TGGLFVQPTVFDGVNNQMRIASEEIFGPVLSVIGFDTADEAVAIANDSIYGLAAAVWTSN 444

Query: 419 GAAARTFQHHIEVGQVGINI----PIPVPLPFFSFTGWKGSFYG---DLHAYGKQGVRFY 471
              A      +  G V IN      +  P     F G+K S  G    +HA+ K     Y
Sbjct: 445 INTAHKVAKALRAGSVWINHYDGGDMTAP-----FGGFKQSGNGRDKSVHAFDK-----Y 494

Query: 472 TETK 475
           TE K
Sbjct: 495 TELK 498


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: 592
Number of extensions: 29
Number of successful extensions: 6
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: 505
Length adjustment: 34
Effective length of query: 463
Effective length of database: 471
Effective search space:   218073
Effective search space used:   218073
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)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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:

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:

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:

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 preprint on GapMind for carbon sources, or view the source code.

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