GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Shewanella amazonensis SB2B

Align Aldehyde dehydrogenase (EC 1.2.1.3) (characterized)
to candidate 6939342 Sama_3435 aldehyde dehydrogenase (RefSeq)

Query= reanno::Marino:GFF3202
         (533 letters)



>FitnessBrowser__SB2B:6939342
          Length = 506

 Score =  786 bits (2031), Expect = 0.0
 Identities = 370/506 (73%), Positives = 433/506 (85%)

Query: 28  MIYAQPGKDGSVVSFKSRYENYIGGEWVAPVKGQYFENITPVTGNVICEIPRSSAEDIDL 87
           MIY+ PG  G++ SFK+RY+N+IGG+WV PV G+YF+N++PV G V C+  RS   DI+L
Sbjct: 1   MIYSAPGTAGAIASFKARYDNFIGGKWVPPVGGEYFDNVSPVDGKVFCQAARSDYRDIEL 60

Query: 88  ALDAAHKAAPAWGKTSPTERSNILLKIADRIEANLEKLAVAETWDNGKAVRETLNADIPL 147
           ALDAAH A  +WGKTS TERSN+LLKIADR+E +LE+LAV ETW+NGKAVRETLNAD+PL
Sbjct: 61  ALDAAHAAKDSWGKTSVTERSNLLLKIADRVEQHLERLAVVETWENGKAVRETLNADLPL 120

Query: 148 AADHFRYFAGCLRAQEGHMGEIDHNTVAYHFHEPLGVVGQIIPWNFPILMAAWKLGPCLA 207
             DHFRYFAGC+RAQEG   ++D NTV+YH  EPLGVVGQIIPWNFP+LMAAWK+ P LA
Sbjct: 121 FVDHFRYFAGCIRAQEGSAADLDANTVSYHLPEPLGVVGQIIPWNFPLLMAAWKIAPALA 180

Query: 208 AGNCTVLKPAEQTPASILVLMEIIGDLLPPGVLNIVNGYGIEAGQALATSKRIAKIAFTG 267
           AGNC VLKPAEQTPASI+VL+E I DLLPPGVLN+VNG+G EAG ALATSKRIAK+AFTG
Sbjct: 181 AGNCVVLKPAEQTPASIMVLLETIEDLLPPGVLNVVNGFGAEAGAALATSKRIAKLAFTG 240

Query: 268 STPVGSHILKCAAENIIPSTVELGGKSPNIYFSDVMKAEPEFIDKCVEGLVLAFFNQGEV 327
           ST VG+HILKCAAEN+IPSTVELGGKSPNIYF+DVM  E  ++DK +EG++LAFFNQGEV
Sbjct: 241 STEVGNHILKCAAENLIPSTVELGGKSPNIYFADVMNHEDNYLDKAIEGMLLAFFNQGEV 300

Query: 328 CTCPSRALVQEDMFEEFMQKVVQRTKSIKRGNPLDTDVQVGAQASKEQFDKIMSYLAIGK 387
           CTCPSR LVQE +++ F++KV+ R K+I++G+PLDTD QVGAQAS+EQ+DKI+ YL IG+
Sbjct: 301 CTCPSRVLVQESIYDAFIEKVIARAKTIRQGSPLDTDTQVGAQASREQYDKILGYLDIGR 360

Query: 388 EEGAVVLTGGDREHLDEEFNNGFYIQPTLFKGDNKMRVFQEEIFGPVVGVTTFKTEEEAL 447
            EGA VL GG+ +  D     G+YIQPT+ KG NKMRVFQEEIFGPVV VTTFK E EAL
Sbjct: 361 AEGAKVLMGGEFKLQDGPEKGGYYIQPTILKGHNKMRVFQEEIFGPVVSVTTFKDEAEAL 420

Query: 448 AIANDTEFGLGAGVWTRDTNLAYRMGRNIQAGRVWMNCYHAYPAHAAFGGYKKSGVGRET 507
           AIANDT++GLGAGVWTRD NLA RMGR IQAGRVW+NCYHAYPAHAAFGGYKKSG+GRET
Sbjct: 421 AIANDTQYGLGAGVWTRDMNLAQRMGRGIQAGRVWINCYHAYPAHAAFGGYKKSGIGRET 480

Query: 508 HKMALEHYQQTKCMLTSYDTNPLGFF 533
           HKM L HYQ TK +L S+DTNPLGFF
Sbjct: 481 HKMMLSHYQNTKNLLVSFDTNPLGFF 506


Lambda     K      H
   0.319    0.136    0.412 

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: 853
Number of extensions: 32
Number of successful extensions: 1
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: 533
Length of database: 506
Length adjustment: 35
Effective length of query: 498
Effective length of database: 471
Effective search space:   234558
Effective search space used:   234558
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 (21.7 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