GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Shewanella amazonensis SB2B

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate 6939342 Sama_3435 aldehyde dehydrogenase (RefSeq)

Query= BRENDA::B6ECN9
         (505 letters)



>FitnessBrowser__SB2B:6939342
          Length = 506

 Score =  324 bits (831), Expect = 4e-93
 Identities = 188/484 (38%), Positives = 281/484 (58%), Gaps = 22/484 (4%)

Query: 14  FIDGEWREPLKKNRLPIINPANEEIIGYIPAATEEDVDMAVKAARSALRRDDWGSTTGAQ 73
           FI G+W  P+       ++P + ++      +   D+++A+ AA +A  +D WG T+  +
Sbjct: 22  FIGGKWVPPVGGEYFDNVSPVDGKVFCQAARSDYRDIELALDAAHAA--KDSWGKTSVTE 79

Query: 74  RAKYLRAIAAKVLEKKPELATLETIDNGKPWFEAAS-DIDDVVACFEYYADLAEALDSKK 132
           R+  L  IA +V +    LA +ET +NGK   E  + D+   V  F Y+A    A +   
Sbjct: 80  RSNLLLKIADRVEQHLERLAVVETWENGKAVRETLNADLPLFVDHFRYFAGCIRAQEG-- 137

Query: 133 QTEVKLHLDSFKTHVLREPLGVVGLITPWNYPLLMTTWKVAPALAAGCAAILKPSELASI 192
            +   L  ++   H L EPLGVVG I PWN+PLLM  WK+APALAAG   +LKP+E    
Sbjct: 138 -SAADLDANTVSYH-LPEPLGVVGQIIPWNFPLLMAAWKIAPALAAGNCVVLKPAEQTPA 195

Query: 193 TSLELGEICREVGLPPGALSILTGLGHEAGSPLVSHPDVDKIAFTGSGPTGVKIMTAAAQ 252
           + + L E   ++ LPPG L+++ G G EAG+ L +   + K+AFTGS   G  I+  AA+
Sbjct: 196 SIMVLLETIEDL-LPPGVLNVVNGFGAEAGAALATSKRIAKLAFTGSTEVGNHILKCAAE 254

Query: 253 LVKPVTLELGGKSPIVVFDDIHN-----LDTAVEWTLFGCFWTNGQICSATSRLIIQETI 307
            + P T+ELGGKSP + F D+ N     LD A+E  L   F+  G++C+  SR+++QE+I
Sbjct: 255 NLIPSTVELGGKSPNIYFADVMNHEDNYLDKAIEGMLLA-FFNQGEVCTCPSRVLVQESI 313

Query: 308 APQFLARLLEWTKNIKISDPLEEDCKLGPVISRGQYEKILKFISTAKDEGATILYGG--- 364
              F+ +++   K I+   PL+ D ++G   SR QY+KIL ++   + EGA +L GG   
Sbjct: 314 YDAFIEKVIARAKTIRQGSPLDTDTQVGAQASREQYDKILGYLDIGRAEGAKVLMGGEFK 373

Query: 365 --DRPEHLKKGYYIQPTIITDVDTSMEIWKEEVFGPVLCVKTFKTEEEAIELANDTKFGL 422
             D PE  K GYYIQPTI+      M +++EE+FGPV+ V TFK E EA+ +ANDT++GL
Sbjct: 374 LQDGPE--KGGYYIQPTILKG-HNKMRVFQEEIFGPVVSVTTFKDEAEALAIANDTQYGL 430

Query: 423 GAAILSKDLERCERFTKAFQSGIVWINCSQPCFWQPPWGGKKRSGFGRELGEWSLENYLN 482
           GA + ++D+   +R  +  Q+G VWINC         +GG K+SG GRE  +  L +Y N
Sbjct: 431 GAGVWTRDMNLAQRMGRGIQAGRVWINCYHAYPAHAAFGGYKKSGIGRETHKMMLSHYQN 490

Query: 483 IKQV 486
            K +
Sbjct: 491 TKNL 494


Lambda     K      H
   0.318    0.136    0.421 

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: 652
Number of extensions: 28
Number of successful extensions: 7
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: 505
Length of database: 506
Length adjustment: 34
Effective length of query: 471
Effective length of database: 472
Effective search space:   222312
Effective search space used:   222312
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.

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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