GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Phaeo:GFF2392 PGA1_c24230 acetylornithine
           aminotransferase ArgD
          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.

Links

Downloads

Related tools

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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