GapMind for catabolism of small carbon sources

 

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

Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate 7025943 Shewana3_3091 4-aminobutyrate aminotransferase (RefSeq)

Query= reanno::pseudo6_N2E2:Pf6N2E2_4013
         (425 letters)



>FitnessBrowser__ANA3:7025943
          Length = 425

 Score =  609 bits (1571), Expect = e-179
 Identities = 306/422 (72%), Positives = 348/422 (82%), Gaps = 3/422 (0%)

Query: 1   MSKTNADLMARRTAAVPRGVGQIHPIFAESAKNATVTDVEGREFIDFAGGIAVLNTGHVH 60
           MS TN  LMARR AAV  GVGQIHP+F   A+NATV DVEGREFIDFAGGIAVLNTGH+H
Sbjct: 1   MSTTNDSLMARRQAAVAGGVGQIHPVFTARAENATVWDVEGREFIDFAGGIAVLNTGHLH 60

Query: 61  PKIIAAVTEQLNKLTHTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAV 120
           PK+ AAV  QL   +HTCF VL YE Y+++CEK+N  VPGDFAKKT L T+GSEAVENAV
Sbjct: 61  PKVKAAVAAQLEDFSHTCFMVLGYESYIQVCEKLNQLVPGDFAKKTALFTSGSEAVENAV 120

Query: 121 KIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVS 180
           K+ARA T RAGVIAFT  YHGRTM  L LTGKV PYS GMGLM   +FRA +P  LHGVS
Sbjct: 121 KVARAYTKRAGVIAFTSGYHGRTMAALALTGKVAPYSKGMGLMSANVFRAEFPCALHGVS 180

Query: 181 IDDSIASIERIFKNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIAD 240
            DD++ASIERIFKNDAEP +IAAII+EPVQGEGGFY A  EFM+RLRALCD+ GI+LIAD
Sbjct: 181 DDDAMASIERIFKNDAEPSNIAAIILEPVQGEGGFYAASPEFMQRLRALCDREGIMLIAD 240

Query: 241 EVQTGAGRTGTFFAMEQMGVAADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYA 300
           EVQTGAGRTGTFFAMEQMGV+AD+TTFAKSIAGGFPL+G+ GKAE MDAI PGGLGGTY 
Sbjct: 241 EVQTGAGRTGTFFAMEQMGVSADITTFAKSIAGGFPLSGITGKAEVMDAIGPGGLGGTYG 300

Query: 301 GSPIACAAALAVMEVFEEEHLLDRCKAVGERLVAGLKAIQKKYPVIGDVRALGAMIAVEL 360
           G+P+ACAAALAV+EVFEEE LL+R  A+GER+ + L  +Q ++P I DVR LGAMIA+EL
Sbjct: 301 GNPLACAAALAVLEVFEEEKLLERANAIGERIKSALNTMQVEHPQIADVRGLGAMIAIEL 360

Query: 361 FENGDSHKPNAAAVAQVVAKARDKGLILLSCGTYGNVLRVLVPLTAPDEQLDKGLAILEE 420
            E G   KP     AQ++A+AR++GLILLSCGTYGNVLR+LVPLT PDEQL  GL IL+ 
Sbjct: 361 MEEG---KPAPQYCAQILAEARNRGLILLSCGTYGNVLRILVPLTVPDEQLAAGLGILKS 417

Query: 421 CF 422
           CF
Sbjct: 418 CF 419


Lambda     K      H
   0.320    0.137    0.395 

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: 666
Number of extensions: 18
Number of successful extensions: 3
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: 425
Length of database: 425
Length adjustment: 32
Effective length of query: 393
Effective length of database: 393
Effective search space:   154449
Effective search space used:   154449
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: 51 (24.3 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