GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate WP_068172105.1 HTA01S_RS13080 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme

Query= reanno::pseudo3_N2E3:AO353_08585
         (454 letters)



>NCBI__GCF_001592305.1:WP_068172105.1
          Length = 454

 Score =  297 bits (760), Expect = 5e-85
 Identities = 161/423 (38%), Positives = 241/423 (56%), Gaps = 8/423 (1%)

Query: 22  PFSDFKQLKEKGPRIITNAKGVYLWDSEGNKILDGMAGLWCVAIGYGRDELADAASKQMR 81
           P +    +K+  P I+   +G ++WD +G+K+LDG+ GLW   +G+    + DA   Q+ 
Sbjct: 18  PMAHPAAMKKAKPDIVARGEGCWIWDVDGHKLLDGVGGLWASNLGHSATAVRDAIVAQLD 77

Query: 82  ELPYYNLFFQTAHPPVLEL-AKAISDIAPEGMNHVFFTGSGSEGNDTMLRMVRHYWAIKG 140
           ELP+YN F  T HP  +EL A+ +  + P+G+  V F+  GS+  +T L++ R Y  ++G
Sbjct: 78  ELPFYNTFRGTTHPRAIELSARLVKLMEPDGVASVMFSSGGSDAVETALKLARQYHKLRG 137

Query: 141 QPNKKVIISRINGYHGSTVAGASLGGMTYMHEQGDLPIPGIVHIPQPYWFGEGGDMTPEE 200
           + ++   IS   GYHG    G S+ G T      +  +PG  HI  P+ +       P E
Sbjct: 138 EKDRFKFISLRQGYHGVHFGGMSVNGNTNFRRAYEPLLPGCFHIDTPWLYRNPYTDDPLE 197

Query: 201 FGIWAANQLEEKILELGVDTVGAFIAEPIQGAGGVIIPPDSYWPRIKEILAKYDILFVAD 260
            G   A  LE +I+  G DTV AFIAEP+QGAGGVI+PP +YWP +++I  K+ +L +AD
Sbjct: 198 LGEICAELLEREIVFQGPDTVAAFIAEPVQGAGGVIVPPANYWPLVRKICDKHGVLLIAD 257

Query: 261 EVICGFGRTGEWFGSDFYGLKPDMMTIAKGLTSGYIPMGGLIVRDEVVEVLNEG----GD 316
           EV+ GFGRTG  FG+  +G+  DM  +AKG++SGY+P+G   +  +V +V N+       
Sbjct: 258 EVVTGFGRTGHLFGTRLWGVNADMWCLAKGISSGYVPLGATAISAKVSQVFNDDKTGQAA 317

Query: 317 FNHGFTYSGHPVAAAVALENIRILREEKIIEHVRAETAPYLQKRLRELNDH-PLVGEVRG 375
             HG+TYS HPV AA AL  +  + E   +          +Q+RLR+L      VG VRG
Sbjct: 318 VGHGYTYSAHPVGAAAALATLDQI-EALDVPGNAGRVGAVMQERLRKLEQTCSFVGNVRG 376

Query: 376 VGLLGAIELVQDKATRARYV-GKGVGMICRQFCFDNGLIMRAVGDTMIIAPPLVITKAEI 434
           VGL+  IE+V DKA R        +     +  +  GL++R  G  +I++PPLVI+  EI
Sbjct: 377 VGLMLGIEMVDDKALRTPMPRSNDIPARVAKEAYQRGLMVRISGPNLILSPPLVISLEEI 436

Query: 435 DEL 437
           + L
Sbjct: 437 NHL 439


Lambda     K      H
   0.320    0.140    0.428 

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: 565
Number of extensions: 32
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: 454
Length of database: 454
Length adjustment: 33
Effective length of query: 421
Effective length of database: 421
Effective search space:   177241
Effective search space used:   177241
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: 51 (24.3 bits)

This GapMind analysis is from Apr 09 2024. 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