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 H281DRAFT_04057 H281DRAFT_04057 acetylornithine aminotransferase apoenzyme
Query= SwissProt::P22256 (426 letters) >FitnessBrowser__Burk376:H281DRAFT_04057 Length = 394 Score = 174 bits (440), Expect = 6e-48 Identities = 131/398 (32%), Positives = 196/398 (49%), Gaps = 45/398 (11%) Query: 35 VWDVEGREYLDFAGGIAVLNTGHLHPKVVAAVEAQLKKLSHTCFQVLAYEPYLELCEIMN 94 ++D G+ YLDF G AV GH ++ A+ Q K L + EP +L ++ Sbjct: 30 LYDNNGKRYLDFIQGWAVNCLGHCDEGMIEALNQQAKLLFNPS-PAFYNEPMAKLAALLT 88 Query: 95 QKVPGDFAKKTLLVTTGSEAVENAVKIARAATKRSGT-----IAFSGAYHGRTHYTLALT 149 Q D K +G+EA E A+K+AR K+ I F ++HGRT T++ + Sbjct: 89 QHSCFD---KVFFANSGAEANEGAIKLARKWGKKFKDGAFEIITFDHSFHGRTLATMSAS 145 Query: 150 GKVNPYSAGMGLMPGHVYRALYPCPLHGISEDDA--IASIHRIFKNDAAPEDIAAIVIEP 207 GK PG + +Y + G + D IAS+ ++ A+++EP Sbjct: 146 GK-----------PG--WDTIYAPQVPGFPKADLNDIASVEKLINAKTV-----AVMLEP 187 Query: 208 VQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSGAGRTGTLFAMEQMGVAPDLTTFA 267 +QGEGG ++ FMQ+LR L +H ++LI DEVQSG GR GTLFA E GV PD+ T Sbjct: 188 IQGEGGVIPATREFMQQLRELTRKHNVLLIVDEVQSGCGRAGTLFAYELSGVEPDIMTLG 247 Query: 268 KSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNPIACVAALEVLKVFEQENLLQKANDL 327 K I GG PLA + +AEV G GGTY GNP+ V+ L+ Sbjct: 248 KGIGGGVPLAALLAKAEVA-VFEAGDQGGTYNGNPLMTAVGYSVISQLTAPGFLEGVRAR 306 Query: 328 GQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELFEDGDHNKPDAKLTAEIVARARD---KG 384 G+ L+ LL ++E+ G+ RG G + A+ L +D + +IV +ARD G Sbjct: 307 GEYLRAKLLELSEERGFKGE-RGEGLLRALLLGKD---------IGNQIVEKARDMQPDG 356 Query: 385 LILLSCGPYYNVLRILVPLTIEDAQIRQGLEIISQCFD 422 L+L + P N+LR + L + + +I Q + ++ D Sbjct: 357 LLLNAARP--NLLRFMPALNVTNEEIDQMMAMLRSILD 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: 427 Number of extensions: 28 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: 394 Length adjustment: 31 Effective length of query: 395 Effective length of database: 363 Effective search space: 143385 Effective search space used: 143385 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