GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lat in Klebsiella michiganensis M5al

Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate BWI76_RS26375 BWI76_RS26375 aspartate aminotransferase family protein

Query= SwissProt::Q5JEW1
         (445 letters)



>FitnessBrowser__Koxy:BWI76_RS26375
          Length = 421

 Score =  258 bits (660), Expect = 2e-73
 Identities = 145/407 (35%), Positives = 224/407 (55%), Gaps = 17/407 (4%)

Query: 40  IERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFYENA 99
           +E+ E   ++D++GN   DFA+G+ V+N GH HP+++ A+++Q + FTH +     YE+ 
Sbjct: 26  VEKAENATLWDIEGNEVIDFAAGIAVLNTGHRHPKIIAAVEQQLQAFTHTAYQIVPYESY 85

Query: 100 IILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKYGTGRKQFLAFYHAFHGRTQAVL 159
           + LAE++  LAP D   K  +  +GAEA E A+K+ +  TGR   + F   FHGRT   +
Sbjct: 86  VTLAERINALAPIDGPAKTAFFTTGAEAVENAVKIARAYTGRPGLITFGGGFHGRTFMTM 145

Query: 160 SLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDFIEEYVFRHV 219
           +LT      + GF P    V H  YPN        D  +  D +               +
Sbjct: 146 ALTGKVAPYKIGFGPFPGSVYHAVYPNAAHGITTADAMKSLDRIFK-----------ADI 194

Query: 220 PPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIGRTGKFWAIE 279
              ++ AI  EPIQGEGG+ V P  F +AL+   D +GILL  DEVQ G  RTGK +A++
Sbjct: 195 AADQVAAIVLEPIQGEGGFNVAPPEFMQALRALCDTHGILLIADEVQTGFARTGKLFAMQ 254

Query: 280 HFGVEPDLIQFGKAIGGGLPLAGVIHRADI-TFDKPGRHATTFGGNPVAIAAGIEVVEIV 338
           H+ V+PDL+   K++ GG PL+GV+ RA++     PG    T+ GNP+A+AA   V++++
Sbjct: 255 HYDVKPDLMTMAKSLAGGFPLSGVVGRAEVMDAPAPGGLGGTYAGNPLAVAAAHAVLDVI 314

Query: 339 KE--LLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVEIVKSKETKEKYPELRDR 396
           +E  L    + +G +L + L + ++    I D RG G   AVE     +T E   E+  +
Sbjct: 315 EEEQLCQRAERLGSHLKEVLNQARQSCPAIADVRGQGSMVAVEF-NDPQTGEPSAEITRQ 373

Query: 397 IVKESAKRGLVLLGCG--DNSIRFIPPLIVTKEEIDVAMEIFEEALK 441
           I +++ + GL+LL CG   N IRF+ PL +   +   A++I    LK
Sbjct: 374 IQQKAQENGLLLLSCGVYGNVIRFLYPLTIPDAQFTKALDILARVLK 420


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: 462
Number of extensions: 29
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: 421
Length adjustment: 32
Effective length of query: 413
Effective length of database: 389
Effective search space:   160657
Effective search space used:   160657
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: 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