GapMind for catabolism of small carbon sources

 

Alignments for a candidate for putA in Shewanella sp. ANA-3

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate 7023012 Shewana3_0250 aldehyde dehydrogenase (RefSeq)

Query= BRENDA::Q9K9B2
         (515 letters)



>FitnessBrowser__ANA3:7023012
          Length = 506

 Score =  218 bits (556), Expect = 3e-61
 Identities = 151/430 (35%), Positives = 222/430 (51%), Gaps = 27/430 (6%)

Query: 76  EKAIQSADEAFQTWRNVNPEERANILVKAAAIIRRRKHEFSAWLVHEAGKPWKEA-DADT 134
           E A+ +A  A   W   +  ERAN+L++ A  + +     +     E GK  +E  +AD 
Sbjct: 59  ELALDAAHAAKDAWGKTSVTERANLLLRIADRVEQNLEYLAVAETWENGKAVRETLNADL 118

Query: 135 AEAIDFLEYYARQMIELNRGKEILSRPGEQNRYFYTPMGVTVTISPWNFALAIMVGTAVA 194
              +D   Y+A   I    G          + +F  P+GV   I PWNF L +M    +A
Sbjct: 119 PLFVDHFRYFAG-CIRAQEGSAADIDGNTVSYHFPEPLGVVGQIIPWNFPL-LMAAWKIA 176

Query: 195 P-IVTGNTVVLKPASTTPVVAAKFVEVLEDAGLPKGVINYVPGSGAEVGDYLVDHPKTSL 253
           P +  GN VVLKPA  TPV     +E++ED  LP G++N V G GAE G  L    + + 
Sbjct: 177 PALAAGNCVVLKPAEQTPVSILVLLELIEDL-LPPGILNVVNGFGAEAGQALATSKRIAK 235

Query: 254 ITFTGSKDVGVRLYERAAVVRPGQNHLKRVIVEMGGKDT------VVVDRDADLDLAAES 307
           + FTGS +VG  + + AA        L    VE+GGK        V+   D  LD A E 
Sbjct: 236 LAFTGSTEVGYHILKCAA------ESLIPSTVELGGKSPNLYFADVMDHEDEYLDKAVEG 289

Query: 308 ILVSAFGFSGQKCSAGSRAVIHKDVYDEVLEKTVALAKNLTVGDPTNRDNYMGPVIDEKA 367
           +L++ F   G+ C+  SR +I + +YD  +EK +A A+ +  G+P +    +G    ++ 
Sbjct: 290 MLLAFFN-QGEVCTCPSRVLIQESIYDRFIEKVLARAQTIKQGNPLDTATQVGAQASQEQ 348

Query: 368 FEKIMSYIEIGKKEG-RLMTGG-----EGDSSTGFFIQPTIIADLDPEAVIMQEEIFGPV 421
           F+KI+SY+ IGK EG +++ GG     EGD S G++I PTI+   + +  I QEEIFGPV
Sbjct: 349 FDKILSYLAIGKDEGAQVLLGGSLCQLEGDQSKGYYISPTIMKGHN-KMRIFQEEIFGPV 407

Query: 422 VAFSKANDFDHALEIANNTEYGLTGAVITRNRAHIEQAKREFHVGNLYFNRNCTGAIVGY 481
           ++ +   D   AL IAN+TEYGL   V TR+    ++  R    G ++   NC  A   +
Sbjct: 408 ISVTTFKDEAEALAIANDTEYGLGAGVWTRDMNRAQRLGRGIQAGRVWI--NCYHAYPAH 465

Query: 482 HPFGGFKMSG 491
             FGG+K SG
Sbjct: 466 AAFGGYKKSG 475


Lambda     K      H
   0.316    0.134    0.388 

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: 615
Number of extensions: 34
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: 515
Length of database: 506
Length adjustment: 35
Effective length of query: 480
Effective length of database: 471
Effective search space:   226080
Effective search space used:   226080
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 (21.6 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