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 6938908 Sama_3011 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein (RefSeq)
Query= SwissProt::P22256 (426 letters) >FitnessBrowser__SB2B:6938908 Length = 404 Score = 215 bits (547), Expect = 2e-60 Identities = 140/392 (35%), Positives = 206/392 (52%), Gaps = 34/392 (8%) Query: 29 RAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAAVEAQLKKLSHTCFQVLAYEPYLE 88 R E RVWD +G EY+DFAGGIAV GH HP +V A++ Q +KL H + EP L Sbjct: 29 RGEGSRVWDQQGTEYVDFAGGIAVNCLGHCHPALVGALKEQGEKLWHLS-NTMTNEPALA 87 Query: 89 LCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIARA-ATKRSG-----TIAFSGAYHGRT 142 L + V FA + +G+EA E A+K+AR A ++ G IAF A+HGRT Sbjct: 88 LA---TKLVEATFADRVYFANSGAEANEAALKLARRYAIEKFGEHKVEVIAFDKAFHGRT 144 Query: 143 HYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISEDDAIASIHRIFKNDAAPEDIAA 202 +T+++ G+ YS G G P A+ P + I+ +A S ++ A Sbjct: 145 FFTVSVGGQA-AYSDGFGPKPA----AITHLPFNDIAALEAAVS-----------DNTCA 188 Query: 203 IVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSGAGRTGTLFAMEQMGVAPD 262 I++EP+QGEGG P F++ +R L D+H ++I DEVQ+G GRTG L+A + PD Sbjct: 189 IMLEPLQGEGGIINGDPEFLRAVRRLADKHNALVIFDEVQTGVGRTGDLYAYMGTEIVPD 248 Query: 263 LTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNPIACVAALEVLKVFEQENLLQ 322 + T AK++ GGFP+A + A++ + G G TY GNP+AC V+ V +L Sbjct: 249 ILTTAKALGGGFPIAAMLTTADIASHLKVGTHGSTYGGNPLACAIGNAVMDVVNTPEVLD 308 Query: 323 KANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELFEDGDHNKPDAKLTAEIVARARD 382 Q +DGL I EK+ ++RG G ++ L N+ A + + + + Sbjct: 309 GVKHREQLFRDGLAQINEKYHVFSEIRGKGLLLGAVL------NEQFAGRSRDFLNASVA 362 Query: 383 KGLILLSCGPYYNVLRILVPLTIEDAQIRQGL 414 +GL+ L G NV+R L I +A I +GL Sbjct: 363 EGLLTLMAGA--NVVRFTPSLVIPEADIVEGL 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: 458 Number of extensions: 17 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: 404 Length adjustment: 31 Effective length of query: 395 Effective length of database: 373 Effective search space: 147335 Effective search space used: 147335 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