GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pad-dh in Shewanella loihica PV-4

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate 5208455 Shew_0967 aldehyde dehydrogenase (RefSeq)

Query= BRENDA::P05091
         (517 letters)



>FitnessBrowser__PV4:5208455
          Length = 498

 Score =  398 bits (1022), Expect = e-115
 Identities = 214/480 (44%), Positives = 297/480 (61%), Gaps = 4/480 (0%)

Query: 34  VFCNQIFINNEWHDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPW 93
           V   Q FIN E+  A S  TF  ++P  G V+ QVA  D  D ++AV  AR  F+ G  W
Sbjct: 18  VIQGQAFINGEYCAADSNDTFDCISPIDGRVLTQVASCDLLDANRAVANAREVFERGD-W 76

Query: 94  RRMDASHRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWA 153
            ++    R +++ R ADL+E +R  LA LETLD GKP   S  VD+    + LR+     
Sbjct: 77  SQLPPVKRKQVMIRFADLLEANRDELALLETLDMGKPIRYSGAVDVAGAARALRWSGEAV 136

Query: 154 DKYHGKTIPIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQ 213
           DK + +  P   +       EPVGV   I+PWNFPLLM  WKLGPALATGN VV+K +E+
Sbjct: 137 DKIYDEIAPTAHNEIGMITREPVGVVAAIVPWNFPLLMACWKLGPALATGNSVVLKPSEK 196

Query: 214 TPLTALYVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVA 273
           +PLTA+ +A L  EAG P GV+N++PG+G T G A+A H DVD + FTGST+I + + + 
Sbjct: 197 SPLTAIRMAQLAIEAGIPKGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMIY 256

Query: 274 AGSSNLKRVTLELGGKSPNIIMSDA-DMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIY 332
           AG SN+KRV LE GGKSPNI+ +DA ++  A   A  A+ FNQG+ C AGSR  V+  + 
Sbjct: 257 AGESNMKRVWLEAGGKSPNIVFNDAPNLKEAAIAAASAIAFNQGEVCTAGSRLLVESGVK 316

Query: 333 DEFVERSVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGG--I 390
           +E +    A  ++   G+P D  T  G  VD+ Q + +L YI  G  EGA+L  GG   +
Sbjct: 317 EELINLIEAEMQAWQPGHPLDPATTCGAVVDQQQLENVLRYIRAGVAEGAQLRQGGQQVL 376

Query: 391 AADRGYFIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAAVFT 450
           A   G ++ PT+F +V++ MTIAKEEIFGPV+ ++ F  +EE +   N++ YGLAA V+T
Sbjct: 377 AETGGVYVAPTIFANVKNEMTIAKEEIFGPVLSVITFDGMEEAIRIGNDTIYGLAAGVWT 436

Query: 451 KDLDKANYLSQALQAGTVWVNCYDVFGAQSPFGGYKMSGSGRELGEYGLQAYTEVKTVTV 510
            D+ KA+  ++AL++G VW+N YD     +PFGGYK SG+GR+   +    YTE+K   +
Sbjct: 437 SDISKAHKTAKALRSGMVWINHYDGGDMTAPFGGYKQSGNGRDKSLHAFDKYTEIKATWI 496


Lambda     K      H
   0.319    0.136    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: 601
Number of extensions: 26
Number of successful extensions: 4
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: 517
Length of database: 498
Length adjustment: 34
Effective length of query: 483
Effective length of database: 464
Effective search space:   224112
Effective search space used:   224112
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