GapMind for catabolism of small carbon sources

 

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

Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate 5210744 Shew_3172 4-aminobutyrate aminotransferase (RefSeq)

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



>FitnessBrowser__PV4:5210744
          Length = 426

 Score =  468 bits (1205), Expect = e-136
 Identities = 234/423 (55%), Positives = 294/423 (69%), Gaps = 1/423 (0%)

Query: 4   TNADLMARRTAAVPRGVGQIHPIFAESAKNATVTDVEGREFIDFAGGIAVLNTGHVHPKI 63
           +NA+L AR+  A+ RG G  +P++ E A NA + DVEG+ +IDF  GIAV NTGH HPK+
Sbjct: 2   SNAELQARKVQAIARGQGNAYPVYVERALNAELWDVEGKRYIDFGTGIAVCNTGHSHPKV 61

Query: 64  IAAVTEQLNKLTHTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAVKIA 123
           +AAV  QL+  +HTC  V  YE  V L E++N   PG   KK + VTTG+EAVEN VKIA
Sbjct: 62  VAAVKAQLDNFSHTCVMVNPYESAVALAEQLNRIAPGGSDKKAIFVTTGAEAVENCVKIA 121

Query: 124 RAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVSIDD 183
           RA TGR GVIAF G +HGRT +T+ LTGK+ PY    G   G IF A YP   HGVS+ D
Sbjct: 122 RAHTGRRGVIAFNGGFHGRTNLTMALTGKITPYKHQFGPFAGDIFHAPYPVAFHGVSVKD 181

Query: 184 SIASIERIFKNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIADEVQ 243
           S+ +IE +FK D  P D+AAI++EPVQGEGGFY AP EF++ LRALCDQHGI+L+ DE+Q
Sbjct: 182 SLKAIEHLFKVDIAPCDVAAIVVEPVQGEGGFYAAPPEFLQALRALCDQHGIVLVMDEIQ 241

Query: 244 TGAGRTGTFFAMEQMGVAADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSP 303
           TG GRTG  F+ E  GV  DL T AK IAGGFPLA V GK+E MDA  PGGLGGTY GSP
Sbjct: 242 TGFGRTGKMFSCEHAGVEPDLMTMAKGIAGGFPLAAVVGKSEIMDAPLPGGLGGTYGGSP 301

Query: 304 IACAAALAVMEVFEEEHLLDRCKAVGERLVAGLKAIQKKYP-VIGDVRALGAMIAVELFE 362
           + C AALAV+EV +EE L++R   +G+     L A++++YP +IG+VR  GAMIA+EL  
Sbjct: 302 VGCVAALAVLEVMQEEQLVERAVKIGDSFNQALSALKEQYPQLIGEVRNQGAMIAMELVI 361

Query: 363 NGDSHKPNAAAVAQVVAKARDKGLILLSCGTYGNVLRVLVPLTAPDEQLDKGLAILEECF 422
           +GD  +PN A    ++A A   GL+LL+CG YGNV+R L  LT  DE + +GLA  +  F
Sbjct: 362 DGDIEQPNTALTQAIIANAAAHGLVLLACGFYGNVIRFLPALTISDEIMAEGLAKFKTLF 421

Query: 423 SEL 425
             L
Sbjct: 422 ESL 424


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: 564
Number of extensions: 18
Number of successful extensions: 2
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: 426
Length adjustment: 32
Effective length of query: 393
Effective length of database: 394
Effective search space:   154842
Effective search space used:   154842
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