GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Phaeobacter inhibens BS107

Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate GFF767 PGA1_c07810 aminotransferase class-III

Query= reanno::pseudo3_N2E3:AO353_08585
         (454 letters)



>FitnessBrowser__Phaeo:GFF767
          Length = 457

 Score =  333 bits (855), Expect = 5e-96
 Identities = 183/456 (40%), Positives = 270/456 (59%), Gaps = 12/456 (2%)

Query: 4   KNPQTREWQTLSSEHHLAPFSDFKQLKEKGPRIITNAKGVYLWDSEGNKILDGMAGLWCV 63
           +N Q  +W   S  H     ++F +      R++T   G ++ D +GN++LD  AGL+CV
Sbjct: 3   RNDQLDQWDRDSFFHPSTHLAEFAR-GNLPQRVVTGGTGCHIEDRDGNRMLDAFAGLYCV 61

Query: 64  AIGYGRDELADAASKQMRELPYYNLFFQTAHPPVLELAKAISDIAPEGMNHVFFTGSGSE 123
            +GYGR E+A+A + Q REL YY+ +        + LAK I D AP+ M+ V+F  SGS+
Sbjct: 62  NVGYGRPEIAEAIADQARELAYYHSYVGHGTEASITLAKMIMDRAPDHMSKVYFGLSGSD 121

Query: 124 GNDTMLRMVRHYWAIKGQPNKKVIISRINGYHGSTVAGASLGGMTYMHEQGDLPIPGIVH 183
            N+T ++++ +Y  I G+P KK IISR  GYHGS +   SL G+   H + DLP+  +VH
Sbjct: 122 ANETNIKLIWYYNNILGRPEKKKIISRWRGYHGSGLMTGSLTGLELFHNKFDLPLAQVVH 181

Query: 184 IPQPYWF-GEGGDMTPEEFGIWAANQLEEKILELGVDTVGAFIAEPIQGAGGVIIPPDSY 242
              PY+F  E    +  +F      +LE  I   G DT+ AFI EP+ G GG++ PP  Y
Sbjct: 182 TESPYYFRREDLSQSEADFVAHCVAELEALIAREGADTIAAFIGEPVLGTGGIVPPPAGY 241

Query: 243 WPRIKEILAKYDILFVADEVICGFGRTGEWFGSDFYGLKPDMMTIAKGLTSGYIPMGGLI 302
           WP I+ +L ++DIL VADEV+ GFGR G  FGSD YG++PD++TIAKGLTS Y P+ G I
Sbjct: 242 WPAIQAVLERHDILLVADEVVTGFGRLGTMFGSDHYGMRPDLITIAKGLTSAYAPLSGSI 301

Query: 303 VRDEVVEVLNEGGDFN----HGFTYSGHPVAAAVALENIRILREEKIIEHVRAETAPYLQ 358
           V D++ +VL  G D N    HG+TYS HP+ AA  + N++++ +  ++E+  A  A YL 
Sbjct: 302 VSDKMWQVLERGTDENGPIGHGWTYSAHPIGAAAGVANLKLIDQLGLVENAGAIGA-YLN 360

Query: 359 KRLRE-LNDHPLVGEVRGVGLLGAIELVQDKATRARY-VGKGVG-MICRQFCFDNGLIMR 415
             +R+ L DHP VG++RG G+L A+E V D+  R  +     +G  I  +    + +I R
Sbjct: 361 DEMRKALGDHPNVGDLRGEGMLCAVEFVADRDDRRFFDASDKIGPQIAAKLLEQDSVIAR 420

Query: 416 AV--GDTMIIAPPLVITKAEIDELVTKARKCLDLTL 449
           A+  GD +  APP  +T+ E D +V    + +   L
Sbjct: 421 AMPQGDILGFAPPFCLTRDEADRVVAATHRAVTAVL 456


Lambda     K      H
   0.320    0.140    0.428 

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: 638
Number of extensions: 38
Number of successful extensions: 5
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: 454
Length of database: 457
Length adjustment: 33
Effective length of query: 421
Effective length of database: 424
Effective search space:   178504
Effective search space used:   178504
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