GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Marino:GFF964
          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.

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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:

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:

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