Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate GFF179 PS417_00900 4-aminobutyrate aminotransferase
Query= reanno::pseudo1_N1B4:Pf1N1B4_3440 (406 letters) >FitnessBrowser__WCS417:GFF179 Length = 425 Score = 216 bits (550), Expect = 1e-60 Identities = 141/396 (35%), Positives = 206/396 (52%), Gaps = 34/396 (8%) Query: 36 VWDQSGRELIDFAGGIAVNVLGHAHPALVAALTEQANKLWHVS-NVFTNEPALRLAHKL- 93 V D GRE IDFAGGIAV GH HP ++AA+TEQ NKL H V EP + L K+ Sbjct: 36 VTDVEGREFIDFAGGIAVLNTGHVHPKIIAAVTEQLNKLTHTCFQVLAYEPYVELCEKIN 95 Query: 94 --VDATFAERVFFCNSGAEANEAAFKLARRVAHDRFGTEKYEIVAALNSFHGRTLFTVNV 151 V FA++ +G+EA E A K+AR T + ++A ++HGRT+ T+ + Sbjct: 96 AKVPGDFAKKTLLVTTGSEAVENAVKIARAA------TGRAGVIAFTGAYHGRTMMTLGL 149 Query: 152 GGQS-KYSDGFGPKITGITHVPYND----------LAALKAAVSDKT-----CAVVLEPI 195 G+ YS G G G+ + + +A+++ + A+++EP+ Sbjct: 150 TGKVVPYSAGMGLMPGGVFRALFPNELHGVSDDDAIASIERIFKNDAEPRDIAAIIIEPV 209 Query: 196 QGEGGVLPAELSYLQGARELCDAHNALLVFDEVQTGMGRSGKLFAYQHYGVTPDILTSAK 255 QGEGG A S+++ RELCD H LL+ DEVQTG GR+G FA + GV D+ T AK Sbjct: 210 QGEGGFYVAPKSFMKRLRELCDKHGILLIADEVQTGAGRTGTFFAMEQMGVAADLTTFAK 269 Query: 256 SLGGGFPIAAMLTTEDLAKHLVVGTHGTTYGGNPLACAVAEAVIDVINTPEVLNGVNAKH 315 S+ GGFP+A + + + G G TY G+P+ACA A AV++V +L+ A Sbjct: 270 SIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSPIACAAALAVMEVFEEEHLLDRCKAVG 329 Query: 316 DKFKTRLEQIGEKYGLFTEVRGLGLLLGCVL---SDAWKGKAKDIFNA---AEREGLMIL 369 ++ T L+ I KY + EVR LG ++ L D K A + + A +GL++L Sbjct: 330 ERLVTGLKAIQAKYPVIGEVRALGAMIAVELFDDGDTHKPNAAAVASVVAKAREKGLILL 389 Query: 370 QAGP--DVIRFAPSLVVEDADIDAGLDRFERAAAKL 403 G +V+R L D +D GL E ++L Sbjct: 390 SCGTYGNVLRVLVPLTSPDEQLDKGLAIIEECFSEL 425 Lambda K H 0.320 0.136 0.400 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: 424 Number of extensions: 23 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: 406 Length of database: 425 Length adjustment: 31 Effective length of query: 375 Effective length of database: 394 Effective search space: 147750 Effective search space used: 147750 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 Apr 09 2024. The underlying query database was built on Apr 09 2024.
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