GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mmsA in Shewanella loihica PV-4

Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate 5208455 Shew_0967 aldehyde dehydrogenase (RefSeq)

Query= BRENDA::P42412
         (487 letters)



>lcl|FitnessBrowser__PV4:5208455 Shew_0967 aldehyde dehydrogenase
           (RefSeq)
          Length = 498

 Score =  232 bits (591), Expect = 3e-65
 Identities = 156/476 (32%), Positives = 248/476 (52%), Gaps = 17/476 (3%)

Query: 10  YINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKT--WSKVAVPR 67
           +INGE+  + ++   D ++P    VL QV      D + A   A E F+   WS++   +
Sbjct: 24  FINGEYCAADSNDTFDCISPIDGRVLTQVASCDLLDANRAVANAREVFERGDWSQLPPVK 83

Query: 68  RARILFNFQQLLSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAGAPSLMMGDSL 127
           R +++  F  LL  +++ELA L T++ GK  + +      G       +G     + D +
Sbjct: 84  RKQVMIRFADLLEANRDELALLETLDMGKPIRYSGAVDVAGAARALRWSGEAVDKIYDEI 143

Query: 128 ASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLLTEK 187
           A  A +      R P+GVV  I P+NFP+++ CW    A+A GN+ +LKPSE++PL   +
Sbjct: 144 APTAHNEIGMITREPVGVVAAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTAIR 203

Query: 188 LVELFEKAGLPKGVFNVVYG-AHDVVNGILEHPEIKAISFVGSKPVG-EYVYKKGSENLK 245
           + +L  +AG+PKGV NV+ G  H V   +  H ++  + F GS  +  + +   G  N+K
Sbjct: 204 MAQLAIEAGIPKGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMIYAGESNMK 263

Query: 246 RVQSLTGAKNHTIVLNDA-NLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEFMAKL 304
           RV    G K+  IV NDA NL++       A   + GE C A + + VE G+ +E +  +
Sbjct: 264 RVWLEAGGKSPNIVFNDAPNLKEAAIAAASAIAFNQGEVCTAGSRLLVESGVKEELINLI 323

Query: 305 QEKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRENVSD-DGYF 363
           + ++   + G+ LD     G V+ +   +  L YI  G+ EGA+L   G++ +++  G +
Sbjct: 324 EAEMQAWQPGHPLDPATTCGAVVDQQQLENVLRYIRAGVAEGAQLRQGGQQVLAETGGVY 383

Query: 364 VGPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNSNAIR 423
           V PTIF NV  EMTI K+EIF PVLSVI    ++EAI I N + +   A ++TS+ +   
Sbjct: 384 VAPTIFANVKNEMTIAKEEIFGPVLSVITFDGMEEAIRIGNDTIYGLAAGVWTSDISKAH 443

Query: 424 YFRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKD----SVDFYTRKK 475
              + + +GM+ IN      M   PF G+K S       NG+D    + D YT  K
Sbjct: 444 KTAKALRSGMVWINHYDGGDMT-APFGGYKQS------GNGRDKSLHAFDKYTEIK 492


Lambda     K      H
   0.318    0.136    0.396 

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: 574
Number of extensions: 35
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: 487
Length of database: 498
Length adjustment: 34
Effective length of query: 453
Effective length of database: 464
Effective search space:   210192
Effective search space used:   210192
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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 paper from 2022 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