GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Shewanella loihica PV-4

Align Aldehyde dehydrogenase (EC 1.2.1.3) (characterized)
to candidate 5211158 Shew_3574 aldehyde dehydrogenase (RefSeq)

Query= reanno::psRCH2:GFF2231
         (506 letters)



>FitnessBrowser__PV4:5211158
          Length = 506

 Score =  793 bits (2048), Expect = 0.0
 Identities = 374/506 (73%), Positives = 441/506 (87%)

Query: 1   MIYAQPGTPGAVVSFKPRYGNYIGGEFVPPVKGEYFVNTSPVNGEVIAEFPRSGAEDIEK 60
           MIY++PGT  A+V+F  RY N+IGG++V PV GEYF N SPV+G+V  +  RS   DIE 
Sbjct: 1   MIYSKPGTTDAIVNFNSRYDNFIGGQWVAPVGGEYFDNRSPVDGQVFCQVARSDERDIEL 60

Query: 61  ALDAAHAAADAWGKTSVQDRALILLKIADRIEANLEKLAVAETWDNGKAVRETLNADVPL 120
           ALDAAHAA DAWGKTSV +R+ +LLKIADR+E NLE LAVAETW+NGKAVRETLNAD+PL
Sbjct: 61  ALDAAHAAKDAWGKTSVTERSNLLLKIADRVEQNLEFLAVAETWENGKAVRETLNADLPL 120

Query: 121 AADHFRYFAGCIRAQEGSAAEINEHTAAYHFHEPLGVVGQIIPWNFPLLMAAWKLAPALA 180
             DHFRYFAGCIRAQEGSAA+I+ +T +YHF EPLGVVGQIIPWNFPLLMAAWK+APALA
Sbjct: 121 FVDHFRYFAGCIRAQEGSAADIDNNTVSYHFPEPLGVVGQIIPWNFPLLMAAWKIAPALA 180

Query: 181 AGNCIVLKPAEQTPLSIMVFIEVVGDLLPPGVLNIVQGFGREAGQALATSTRIAKIAFTG 240
           AGNCIVLKPAEQTP+SI+V +E++ DLLP GVLNIV GFG EAGQALA S RIAK+AFTG
Sbjct: 181 AGNCIVLKPAEQTPVSILVMVELIQDLLPAGVLNIVNGFGTEAGQALAVSKRIAKLAFTG 240

Query: 241 STPVGSHIMRCAAENIIPSTVELGGKSPNIFFEDIMNAEPAFIEKAAEGLVLAFFNQGEV 300
           ST +G HI++CAAE++IPSTVELGGKSPNI+F D+M  E  +++KA EG++LAFFNQGEV
Sbjct: 241 STQIGHHILKCAAESLIPSTVELGGKSPNIYFADVMEQEDEYLDKAVEGMLLAFFNQGEV 300

Query: 301 CTCPSRALIQESIFEPFMEVVMKKIKAIKRGNPLDTDTMVGAQASEQQFDKILSYMEIAQ 360
           CTCPSR LI ESI++ F++ V+ + K IK+GNPLDTDT VGAQAS++QFDKILSY+EI +
Sbjct: 301 CTCPSRVLIAESIYDKFIDKVIARAKTIKQGNPLDTDTQVGAQASQEQFDKILSYLEIGR 360

Query: 361 QEGAQILTGGAAEKLEGSLSTGYYVQPTLIKGHNKMRVFQEEIFGPVVGVATFKDEAEAL 420
            EGA++L GG + +L G  S+G+Y++PT++KGHNKMRVFQEEIFGPV+ V TFKDEAEAL
Sbjct: 361 NEGAEVLIGGTSCQLSGDQSSGFYIEPTILKGHNKMRVFQEEIFGPVISVTTFKDEAEAL 420

Query: 421 AIANDTEFGLGAGVWTRDINRAYRMGRGIKAGRVWTNCYHLYPAHAAFGGYKKSGVGRET 480
           AIANDTE+GLGAGVWTRD+NRA RMGRGI+AGRVW NCYH YPAHAAFGGYKKSG+GRET
Sbjct: 421 AIANDTEYGLGAGVWTRDMNRAQRMGRGIQAGRVWINCYHAYPAHAAFGGYKKSGIGRET 480

Query: 481 HKMMLDHYQQTKNLLISYDINPLGFF 506
           HKMML HYQ TKNLL+SYD+NPLGFF
Sbjct: 481 HKMMLSHYQNTKNLLVSYDVNPLGFF 506


Lambda     K      H
   0.319    0.136    0.406 

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: 764
Number of extensions: 17
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: 506
Length of database: 506
Length adjustment: 34
Effective length of query: 472
Effective length of database: 472
Effective search space:   222784
Effective search space used:   222784
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