GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lat in Phaeobacter inhibens BS107

Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate GFF2392 PGA1_c24230 acetylornithine aminotransferase ArgD

Query= SwissProt::Q5JEW1
         (445 letters)



>FitnessBrowser__Phaeo:GFF2392
          Length = 394

 Score =  186 bits (472), Expect = 1e-51
 Identities = 133/413 (32%), Positives = 204/413 (49%), Gaps = 51/413 (12%)

Query: 37  PIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFY 96
           P+   +GEG  + + DG  F D A+G+ V  +GH+HP +V+A+  QAE   H S   +  
Sbjct: 13  PLSFVKGEGAWLIEADGRRFLDLAAGIAVNALGHAHPALVKALTDQAETLWHVSNL-YHI 71

Query: 97  ENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVK---YGTG---RKQFLAFYHA 150
                LA++L+E +  D    V + NSG E+ E A+K+ +   +  G   R + L F  +
Sbjct: 72  PQQQALADRLVEHSFADT---VFFTNSGTESCELAVKMARKYFHDKGQPERVEILTFSGS 128

Query: 151 FHGRTQAVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDF 210
           FHGR+ A +S   S+ +   GF P +PG  H+ + +       +DG      +T+ + D 
Sbjct: 129 FHGRSSAGISAAGSEKMTA-GFGPMLPGFKHLMFGD-------LDG------VTDAITD- 173

Query: 211 IEEYVFRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIG 270
                       +  AI  EP+QGEGG    P    KAL++  DE+G+LL  DEVQ G+G
Sbjct: 174 ------------QTAAILIEPVQGEGGIRPVPDAELKALRQICDEHGLLLILDEVQCGVG 221

Query: 271 RTGKFWAIEHFGVEPDLIQFGKAIGGGLPLAGVIHRADITFD-KPGRHATTFGGNPVAIA 329
           RTGK +A E  G+ PD++   K IGGG PL  V+   +       G H +T+GGNP+  A
Sbjct: 222 RTGKLFAHEWAGITPDIMMVAKGIGGGFPLGAVLATEEAASGMTAGTHGSTYGGNPLGCA 281

Query: 330 AGIEVVEIV--KELLPHVQEVGDYLHKYLEEFKEKYEVIGDA-RGLGLAQAVEIVKSKET 386
            G  V++ V   E L  V      L + LE     +  + +A RG GL   ++ V +   
Sbjct: 282 VGCAVMDHVTDPEFLAEVSRKAGLLRQKLEGLVASHPQVFEAVRGSGLMLGLKCVAANTD 341

Query: 387 KEKYPELRDRIVKESAKRGLVLLGCGDNSIRFIPPLIVTKEEIDVAMEIFEEA 439
                     +V    +  +V +   DN +R +PPL +T E+I  A    ++A
Sbjct: 342 ----------VVAAGYEAEVVTVPAADNVVRLLPPLTLTDEDIAEAFARLDQA 384


Lambda     K      H
   0.320    0.141    0.418 

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: 408
Number of extensions: 21
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: 445
Length of database: 394
Length adjustment: 32
Effective length of query: 413
Effective length of database: 362
Effective search space:   149506
Effective search space used:   149506
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 (21.7 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