GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Pedobacter sp. GW460-11-11-14-LB5

Align 4-aminobutyrate aminotransferase GabT; 5-aminovalerate transaminase; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT; EC 2.6.1.19; EC 2.6.1.48 (characterized)
to candidate CA265_RS15205 CA265_RS15205 aspartate aminotransferase family protein

Query= SwissProt::P22256
         (426 letters)



>FitnessBrowser__Pedo557:CA265_RS15205
          Length = 378

 Score =  195 bits (496), Expect = 2e-54
 Identities = 131/399 (32%), Positives = 202/399 (50%), Gaps = 47/399 (11%)

Query: 29  RAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAAVEAQLKKLSHTCFQVLAYEPYLE 88
           RA+   ++D + ++++D   GI V N GH HP VV A++ Q +   H    ++ Y  Y++
Sbjct: 6   RAKGIYIYDAQNKKHIDLIAGIGVSNVGHCHPAVVKAIQEQAETYMH----LMVYGEYVQ 61

Query: 89  LCEIMNQKVPGDFAKKTLLVT----TGSEAVENAVKIARAATKRSGTIAFSGAYHGRTHY 144
             ++   K   D   ++L  T    +G+EAVE A+K+A+  T R G IA   AYHG T  
Sbjct: 62  TPQVNFAKALADILPESLSCTYFLNSGTEAVEGAMKLAKRYTGRKGFIACKNAYHGSTQG 121

Query: 145 TLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISEDDAIASIHRIFKNDAAPEDIAAIV 204
             +L  + + YS+G G    HV             E + +A + +I        +IAA+ 
Sbjct: 122 AESLM-ESDFYSSGYGPFLPHV----------SFIEHNNLADLEKI------TNEIAAVF 164

Query: 205 IEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSGAGRTGTLFAMEQMGVAPDLT 264
           IEP+QGE G   S  ++MQ LR  C E G +LI DE+QSG GR+G +FA E   V PD+ 
Sbjct: 165 IEPIQGEAGIRVSDLSYMQALRTKCTETGTLLIFDEIQSGFGRSGKMFAFEHYNVVPDVL 224

Query: 265 TFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGG---TYAGNPIACVAALEVLKVFEQENLL 321
             AK I GG P+       E+M  ++   + G   T+ G+P+ C A L  L+    ++++
Sbjct: 225 LLAKGIGGGMPIGAFISSLEIMSVLSHTPILGHMTTFGGHPVCCAAGLATLRTLVDDHIV 284

Query: 322 QKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELFEDGDHNKPDAKLTAEIVARAR 381
            +  + GQ  K  L     +HP I ++RG G M+A+E FE+ + NK       +I+    
Sbjct: 285 DEVEEKGQLFKQLL-----QHPAIKEIRGKGLMLAVE-FENFEINK-------KIIDACI 331

Query: 382 DKGLI---LLSCGPYYNVLRILVPLTIEDAQIRQGLEII 417
             G++    L C    N +RI  PL I   +I +   II
Sbjct: 332 LDGVLSDWFLHCS---NSMRIAPPLIITKEEIAEACTII 367


Lambda     K      H
   0.320    0.137    0.401 

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: 383
Number of extensions: 23
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: 426
Length of database: 378
Length adjustment: 31
Effective length of query: 395
Effective length of database: 347
Effective search space:   137065
Effective search space used:   137065
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