GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pad-dh in Shewanella amazonensis SB2B

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

Query= BRENDA::P05091
         (517 letters)



>FitnessBrowser__SB2B:6939342
          Length = 506

 Score =  375 bits (964), Expect = e-108
 Identities = 208/482 (43%), Positives = 286/482 (59%), Gaps = 18/482 (3%)

Query: 40  FINNEWHDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDAS 99
           FI  +W   V  + F  V+P  G+V CQ A  D  D++ A+ AA AA      W +   +
Sbjct: 22  FIGGKWVPPVGGEYFDNVSPVDGKVFCQAARSDYRDIELALDAAHAA---KDSWGKTSVT 78

Query: 100 HRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHGK 159
            R  LL ++AD +E+    LA +ET +NGK    +   DL + +   RY+AG      G 
Sbjct: 79  ERSNLLLKIADRVEQHLERLAVVETWENGKAVRETLNADLPLFVDHFRYFAGCIRAQEGS 138

Query: 160 TIPIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTAL 219
              +D +  SY   EP+GV GQIIPWNFPLLM AWK+ PALA GN VV+K AEQTP + +
Sbjct: 139 AADLDANTVSYHLPEPLGVVGQIIPWNFPLLMAAWKIAPALAAGNCVVLKPAEQTPASIM 198

Query: 220 YVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGSSNL 279
            +   I++   PPGV+N+V GFG  AGAA+A+ + + K+AFTGSTE+G  I +   + NL
Sbjct: 199 VLLETIEDL-LPPGVLNVVNGFGAEAGAALATSKRIAKLAFTGSTEVGNHI-LKCAAENL 256

Query: 280 KRVTLELGGKSPNIIMSDA------DMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIYD 333
              T+ELGGKSPNI  +D        +D A+E    A FFNQG+ C   SR  VQE IYD
Sbjct: 257 IPSTVELGGKSPNIYFADVMNHEDNYLDKAIEGMLLA-FFNQGEVCTCPSRVLVQESIYD 315

Query: 334 EFVERSVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGGIAAD 393
            F+E+ +ARAK+   G+P D+ T+ G Q    Q+ KILGY++ G+ EGAK+L GG     
Sbjct: 316 AFIEKVIARAKTIRQGSPLDTDTQVGAQASREQYDKILGYLDIGRAEGAKVLMGGEFKLQ 375

Query: 394 -----RGYFIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAAV 448
                 GY+IQPT+     + M + +EEIFGPV+ +  FK   E +  AN++ YGL A V
Sbjct: 376 DGPEKGGYYIQPTILKG-HNKMRVFQEEIFGPVVSVTTFKDEAEALAIANDTQYGLGAGV 434

Query: 449 FTKDLDKANYLSQALQAGTVWVNCYDVFGAQSPFGGYKMSGSGRELGEYGLQAYTEVKTV 508
           +T+D++ A  + + +QAG VW+NCY  + A + FGGYK SG GRE  +  L  Y   K +
Sbjct: 435 WTRDMNLAQRMGRGIQAGRVWINCYHAYPAHAAFGGYKKSGIGRETHKMMLSHYQNTKNL 494

Query: 509 TV 510
            V
Sbjct: 495 LV 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: 658
Number of extensions: 30
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: 517
Length of database: 506
Length adjustment: 35
Effective length of query: 482
Effective length of database: 471
Effective search space:   227022
Effective search space used:   227022
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