GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Shewanella halifaxensis HAW-EB4

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_012278671.1 SHAL_RS18655 aspartate aminotransferase family protein

Query= SwissProt::P22256
         (426 letters)



>NCBI__GCF_000019185.1:WP_012278671.1
          Length = 405

 Score =  218 bits (555), Expect = 3e-61
 Identities = 137/392 (34%), Positives = 205/392 (52%), Gaps = 34/392 (8%)

Query: 29  RAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAAVEAQLKKLSHTCFQVLAYEPYLE 88
           R E  RVWD EG+EY+DFAGGIAV   GH HP +V A++ Q +KL H    V+  EP LE
Sbjct: 29  RGEGSRVWDQEGKEYIDFAGGIAVNCLGHCHPALVGALKTQGEKLWHLS-NVMTNEPALE 87

Query: 89  LCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIARA------ATKRSGTIAFSGAYHGRT 142
           L     + V   FA++     +G+EA E A+K+ R         ++   IAF  A+HGRT
Sbjct: 88  LA---TKLVEATFAERVYFANSGAEANEAALKLVRRYAMDKFGAEKDQIIAFDKAFHGRT 144

Query: 143 HYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISEDDAIASIHRIFKNDAAPEDIAA 202
            +T+++ G+   YS G G  P    +++   P + I   +A+ S           +   A
Sbjct: 145 FFTVSVGGQA-AYSDGFGPKP----QSITHVPFNDIEALEAVFS-----------DKTCA 188

Query: 203 IVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSGAGRTGTLFAMEQMGVAPD 262
           +++EP+QGEGG   + P F++ +RALCD+H  +L+ DEVQ+G GR G L+A  +  V PD
Sbjct: 189 VMMEPLQGEGGIIDADPEFLKAVRALCDKHNALLVFDEVQTGVGRLGELYAYMRGDVVPD 248

Query: 263 LTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNPIACVAALEVLKVFEQENLLQ 322
           + T AK++ GGFP+A +    E+   +  G  G TY GNP+AC     V+ V     +L 
Sbjct: 249 VLTTAKALGGGFPIAAMLTTKEIAAHLKIGTHGSTYGGNPLACAVGNAVMDVVNTPEVLN 308

Query: 323 KANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELFEDGDHNKPDAKLTAEIVARARD 382
                 Q  +DGL  I +K+    ++RG G +I   +      N        E +    +
Sbjct: 309 GVKHREQLFRDGLNKINDKYDVFSEIRGQGLLIGAVV------NSKYQGRAKEFLVAGIN 362

Query: 383 KGLILLSCGPYYNVLRILVPLTIEDAQIRQGL 414
           +G++ L  G   NV+R    L I +  I +GL
Sbjct: 363 EGVMSLVAGA--NVVRFTPSLVIPETDIAEGL 392


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: 435
Number of extensions: 16
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: 405
Length adjustment: 31
Effective length of query: 395
Effective length of database: 374
Effective search space:   147730
Effective search space used:   147730
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