GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gabT in Shewanella oneidensis MR-1

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 199805 SO0617 acetylornithine aminotransferase (NCBI ptt file)

Query= SwissProt::P22256
         (426 letters)



>lcl|FitnessBrowser__MR1:199805 SO0617 acetylornithine
           aminotransferase (NCBI ptt file)
          Length = 405

 Score =  221 bits (562), Expect = 4e-62
 Identities = 143/392 (36%), Positives = 208/392 (53%), Gaps = 34/392 (8%)

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

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

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

Query: 203 IVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSGAGRTGTLFAMEQMGVAPD 262
           I++EP+QGEGG   + PAF++ +R L ++H  ++I DEVQ+G GRTG L+A     + PD
Sbjct: 189 IMLEPLQGEGGIIDADPAFLKAVRELANKHNALVIFDEVQTGVGRTGELYAYMGTDIVPD 248

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

Query: 323 KANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELFEDGDHNKPDAKLTAEIVARARD 382
                 Q L+DGL  I EK+    +VRG G ++   L E       D  L A +      
Sbjct: 309 GVKHREQLLRDGLNKINEKYHVFSEVRGKGLLLGAVLNEQYQGRSRDF-LVASVA----- 362

Query: 383 KGLILLSCGPYYNVLRILVPLTIEDAQIRQGL 414
           +GL+ L  G   NV+R    L I +A I +GL
Sbjct: 363 EGLMSLMAGA--NVVRFAPSLVIPEADIAEGL 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: 456
Number of extensions: 14
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 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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