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 N515DRAFT_3308 N515DRAFT_3308 acetylornithine/N-succinyldiaminopimelate aminotransferase
Query= SwissProt::P22256 (426 letters) >FitnessBrowser__Dyella79:N515DRAFT_3308 Length = 411 Score = 221 bits (562), Expect = 4e-62 Identities = 145/398 (36%), Positives = 204/398 (51%), Gaps = 35/398 (8%) Query: 25 IFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAAVEAQLKKLSHTCFQVLAYE 84 + D + RVWD EGR+Y+D GIAV GH P +V A+ Q +KL H+ V E Sbjct: 27 VVLDHGKGARVWDTEGRDYVDLGAGIAVNALGHQDPDLVDALVTQARKLWHSS-NVFYTE 85 Query: 85 PYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIARAATKRSGT-------IAFSGA 137 P L L E + Q FA++ L +G+EA E A+K+ R G + F G+ Sbjct: 86 PPLHLAEELVQA--SGFAERVFLCNSGTEANEAAIKLVRKWAASKGRAPEQRVILTFRGS 143 Query: 138 YHGRTHYTLALTGKVNP-YSAGMGLMPGHVYRALYPCPLHGISEDDAIASIHRIFKNDAA 196 +HGRT A+T P Y +PG +R L + + +A + F A Sbjct: 144 FHGRT--LAAVTATAQPKYQENYEPLPGG-FRYL---------DFNDVAGLEAAF----A 187 Query: 197 PEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSGAGRTGTLFAMEQ 256 D+AA+++EPVQGEGG +SPAF++R R LCD H +L+ DE+Q G GRTGTLFA Q Sbjct: 188 QGDVAAVMLEPVQGEGGVLPASPAFIRRARELCDTHEALLVLDEIQCGMGRTGTLFAHAQ 247 Query: 257 MGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNPIACVAALEVLKVFE 316 GV PD+ T AK++ GFP+ + +V + + G G T+ GNP+A A L+ Sbjct: 248 DGVTPDIVTLAKALGCGFPIGAMLAGPKVAEVMQYGAHGTTFGGNPMAAAVARVALRKLA 307 Query: 317 QENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELFEDGDHNKPDAKLTAEI 376 L+ Q L+DGL AI + +VRG G M+ L E E+ Sbjct: 308 SAELMANVAKQAQALRDGLAAIDGELKLFAEVRGRGLMLGAVLAEAYKGR------AGEV 361 Query: 377 VARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGL 414 + A GL++L GP +VLR + PL I DA + +GL Sbjct: 362 LDHAAAHGLLVLQAGP--DVLRFVPPLNITDADLAEGL 397 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: 465 Number of extensions: 25 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: 411 Length adjustment: 32 Effective length of query: 394 Effective length of database: 379 Effective search space: 149326 Effective search space used: 149326 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.
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:
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