GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Phaeobacter inhibens BS107

Align 4-aminobutyrate transaminase subunit (EC 2.6.1.19) (characterized)
to candidate GFF2392 PGA1_c24230 acetylornithine aminotransferase ArgD

Query= metacyc::MONOMER-11537
         (425 letters)



>FitnessBrowser__Phaeo:GFF2392
          Length = 394

 Score =  194 bits (492), Expect = 5e-54
 Identities = 139/411 (33%), Positives = 200/411 (48%), Gaps = 50/411 (12%)

Query: 25  PIFADSAKNATVTDVEGREFIDFAGGIAVLNTGHVHPKIIAAVTEQLNKLTHTCFQVLAY 84
           P+     + A + + +GR F+D A GIAV   GH HP ++ A+T+Q   L H     L +
Sbjct: 13  PLSFVKGEGAWLIEADGRRFLDLAAGIAVNALGHAHPALVKALTDQAETLWHV--SNLYH 70

Query: 85  EPYVE-LCEKINAKVPGDFAKKTLLVTTGSEAVENAVKIAR------AATGRAGVIAFTG 137
            P  + L +++   V   FA       +G+E+ E AVK+AR          R  ++ F+G
Sbjct: 71  IPQQQALADRL---VEHSFADTVFFTNSGTESCELAVKMARKYFHDKGQPERVEILTFSG 127

Query: 138 AYHGRTMMTLGLTGKVVPYSAGMG-LMPGGIFRALYPNELHGVSIDDSIASIERIFKNDA 196
           ++HGR+   +   G     +AG G ++PG  F+ L   +L GV+              DA
Sbjct: 128 SFHGRSSAGISAAGSE-KMTAGFGPMLPG--FKHLMFGDLDGVT--------------DA 170

Query: 197 EPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIADEVQTGAGRTGTFFAME 256
                AAI+IEPVQGEGG    P   +K LR +CD+HG+LLI DEVQ G GRTG  FA E
Sbjct: 171 ITDQTAAILIEPVQGEGGIRPVPDAELKALRQICDEHGLLLILDEVQCGVGRTGKLFAHE 230

Query: 257 QMGVTADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSPIACAAALAVMEVF 316
             G+T D+   AK I GGFPL  V    E    +  G  G TY G+P+ CA   AVM+  
Sbjct: 231 WAGITPDIMMVAKGIGGGFPLGAVLATEEAASGMTAGTHGSTYGGNPLGCAVGCAVMDHV 290

Query: 317 EEEHLLDRCKAVGERLVTGLKAIQAKYPVIGE-VRALGAMIAVELFENGDSHKPNAAAVA 375
            +   L         L   L+ + A +P + E VR  G M+ ++            AA  
Sbjct: 291 TDPEFLAEVSRKAGLLRQKLEGLVASHPQVFEAVRGSGLMLGLKC----------VAANT 340

Query: 376 QVVAKARDKGLILLSCGTYGNVLRVLVPLTSPD-------AQLDKGLAIIE 419
            VVA   +  ++ +      NV+R+L PLT  D       A+LD+   ++E
Sbjct: 341 DVVAAGYEAEVVTVPAA--DNVVRLLPPLTLTDEDIAEAFARLDQAATLVE 389


Lambda     K      H
   0.320    0.137    0.394 

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: 419
Number of extensions: 18
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 425
Length of database: 394
Length adjustment: 31
Effective length of query: 394
Effective length of database: 363
Effective search space:   143022
Effective search space used:   143022
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: 50 (23.9 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