GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Jannaschia aquimarina GSW-M26

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 WP_043918626.1 jaqu_RS08900 aspartate aminotransferase family protein

Query= SwissProt::P22256
         (426 letters)



>NCBI__GCF_000877395.1:WP_043918626.1
          Length = 394

 Score =  191 bits (486), Expect = 3e-53
 Identities = 132/388 (34%), Positives = 190/388 (48%), Gaps = 39/388 (10%)

Query: 36  WDVE--GREYLDFAGGIAVLNTGHLHPKVVAAVEAQLKKLSHTCFQVLAYEPYLELCEIM 93
           W VE  GR YLD   GIAV   GH HP +  A+ AQ  +L HT      YE   +  E+ 
Sbjct: 23  WLVERGGRRYLDLGAGIAVNVLGHAHPALTEALTAQAGQLWHTSN---LYE-IPQQQELA 78

Query: 94  NQKVPGDFAKKTLLVTTGSEAVENAVKIARA--ATK---RSGTIAFSGAYHGRTHYTLAL 148
            + V   FA       +G+EA E AVK+AR   +TK   R+  +AF+G++HGR+   +A 
Sbjct: 79  ERLVEATFADTVFFTNSGTEACELAVKMARKYWSTKGEDRATIVAFTGSFHGRSSAGIAA 138

Query: 149 TGKVNPYSAGMGLMPGHVYRALYPCPLHGISEDDAIASIHRIFKNDAAPEDIAAIVIEPV 208
            G          L+PG V+            + DA A + +        +DIAA+++EP+
Sbjct: 139 AGSKKMTDGFGPLLPGFVHVPF--------GDHDAFAEVMK-------RDDIAAVILEPI 183

Query: 209 QGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSGAGRTGTLFAMEQMGVAPDLTTFAK 268
           QGEGG        ++ LR +CD  G ++I DEVQ G GRTG LFA E  GV PD+   AK
Sbjct: 184 QGEGGIVPVPDQCLKGLRDVCDRTGALMILDEVQCGMGRTGKLFAHEWAGVTPDIMMVAK 243

Query: 269 SIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNPIACVAALEVLKVFEQENLLQKANDLG 328
            I GGFPL  +         ++ G  G TY GNP+AC     V++V   E  L +     
Sbjct: 244 GIGGGFPLGALLATEHAAAGMSAGTHGSTYGGNPLACAVGNAVMEVVADEAFLAEVRRKA 303

Query: 329 QKLKDGLLAIAEKHPEIGD-VRGLGAMIAIELFEDGDHNKPDAKLTAEIVARARDKGLIL 387
             L+ GL  +   HP++ + VRG G M+ ++                +++A ARD  +++
Sbjct: 304 GLLRQGLEGLVASHPDVFEVVRGSGLMLGLKC----------RVPVGDVIAAARDAEVLI 353

Query: 388 LSCGPYYNVLRILVPLTIEDAQIRQGLE 415
           +         R+L  L I D  IR+ L+
Sbjct: 354 VPAAD--ETARLLPALNIGDDDIREALD 379


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: 491
Number of extensions: 32
Number of successful extensions: 4
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: 394
Length adjustment: 31
Effective length of query: 395
Effective length of database: 363
Effective search space:   143385
Effective search space used:   143385
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 24 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