Align 2-aminoadipate transaminase; 2-aminoadipate aminotransferase; L-2AA aminotransferase; EC 2.6.1.39 (characterized)
to candidate 5210744 Shew_3172 4-aminobutyrate aminotransferase (RefSeq)
Query= SwissProt::Q88FI7 (416 letters) >FitnessBrowser__PV4:5210744 Length = 426 Score = 340 bits (871), Expect = 6e-98 Identities = 182/409 (44%), Positives = 250/409 (61%), Gaps = 13/409 (3%) Query: 4 ESISQSIAIVHPITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATR 63 ++I++ +P+ + NAE+WD +GKRYIDF GI V N GH +P VV A++AQ Sbjct: 12 QAIARGQGNAYPVYVERALNAELWDVEGKRYIDFGTGIAVCNTGHSHPKVVAAVKAQLDN 71 Query: 64 LTHYAFNAAPHGPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARGATGKRAII 123 +H P+ +AL EQL++ P + +GAEA EN +K+AR TG+R +I Sbjct: 72 FSHTCVMVNPYESAVALAEQLNRIAPGGSDKKAIFVTTGAEAVENCVKIARAHTGRRGVI 131 Query: 124 AFDGGFHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFS 183 AF+GGFHGRT T+ L GK+ PYK + G G ++H PYP A GV+ + +LKA++ LF Sbjct: 132 AFNGGFHGRTNLTMALTGKITPYKHQFGPFAGDIFHAPYPVAFHGVSVKDSLKAIEHLFK 191 Query: 184 VELAVEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRF 243 V++A DVAA + EPVQGEGGF A P F QALR CD+ GI++++DEIQ+GFGRTG+ F Sbjct: 192 VDIAPCDVAAIVVEPVQGEGGFYAAPPEFLQALRALCDQHGIVLVMDEIQTGFGRTGKMF 251 Query: 244 AFPRLGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASL 303 + G+EPDL+ +AK IAGG PL AVVG+ E+M A GGLGGTY G+P+ C AALA L Sbjct: 252 SCEHAGVEPDLMTMAKGIAGGFPLAAVVGKSEIMDAPLPGGLGGTYGGSPVGCVAALAVL 311 Query: 304 AQMTDENL----ATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADG-- 357 M +E L G+ QA+ + E++ IG + GAM +E DG Sbjct: 312 EVMQEEQLVERAVKIGDSFNQALSALKEQY-----PQLIGEVRNQGAMIAMELV-IDGDI 365 Query: 358 -SPAPAQLAKVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGL 405 P A ++ A A GL+L+ G ++IR L LTI E++ EGL Sbjct: 366 EQPNTALTQAIIANAAAHGLVLLACGFYGNVIRFLPALTISDEIMAEGL 414 Lambda K H 0.320 0.137 0.402 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: 529 Number of extensions: 20 Number of successful extensions: 2 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: 416 Length of database: 426 Length adjustment: 32 Effective length of query: 384 Effective length of database: 394 Effective search space: 151296 Effective search space used: 151296 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