Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate Echvi_0577 Echvi_0577 ornithine aminotransferase
Query= reanno::Koxy:BWI76_RS11670 (406 letters) >FitnessBrowser__Cola:Echvi_0577 Length = 413 Score = 228 bits (582), Expect = 2e-64 Identities = 130/389 (33%), Positives = 204/389 (52%), Gaps = 6/389 (1%) Query: 18 YAPAAFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKALTEQAGKFWHTGNG 77 Y P + RGEG +WD +G++Y DF + GH HPR+++ L +QAG T Sbjct: 23 YHPLPVVLSRGEGVFMWDVEGEKYYDFLSSYSAVNQGHCHPRILQTLIDQAGTLTLTSRA 82 Query: 78 YTNEPVLRLAKQLIDATFADRVFFCNSGAEANEAALKLARKYAHDRFG--SEKSGIVAFK 135 + N+ + K L + D+V N+GAE E A+K+ARK+ +++ G + I+ K Sbjct: 83 FHNDVLGPFEKFLTEYFGYDKVLPMNTGAEGVETAIKIARKWGYEKKGIPENEGTIIVAK 142 Query: 136 NAFHGRTLFTVSAGGQPAYSQDFAPLPPQIQHAIYNDLDSAKALIDD--NTCAVIVEPMQ 193 N FHGRT +S ++F P P ++D+D+ K ++ N +VEP+Q Sbjct: 143 NNFHGRTTTVISFSNDETARKNFGPYTPGFVTIPHDDIDALKDVLSQSKNIIGYLVEPIQ 202 Query: 194 GEGGVVPADADFLRGLRELCDAHNALLIFDEVQTGVGRTGELYAYMHYGVTPDLLSTAKA 253 GE GV +L+ + +C H L + DE+QTG+ RTG+L A H GV PD+L KA Sbjct: 203 GEAGVYVPKEGYLKEVAAVCKDHGVLFMADEIQTGIARTGKLLACDHEGVKPDMLILGKA 262 Query: 254 LGGGF-PIGALLASERCASVMTVGTHGTTYGGNPLACAVAGEVFATINTREVLNGVKQRH 312 + GGF P+ A+LA + V+ G HG+T+GGNPL VA + ++ + Sbjct: 263 ISGGFYPVSAVLADDHIMEVIQPGQHGSTFGGNPLGAKVAMTALNVVKDEKLAENADKLG 322 Query: 313 QWFCERLNAINARYGLFKEIRGLGLLIGCVLKD-EYAGKAKAISNQAAEEGLMILIAGAN 371 + F ER+ + + L + +RG GLL V+ D E + A + E GL+ N Sbjct: 323 KLFRERIQQLVDKSDLVELVRGKGLLNAIVINDTEDSDTAWRLCLALKENGLLAKPTHGN 382 Query: 372 VVRFAPALIISEDEVNSGLDRFELACKRF 400 ++RFAP L+I+E++++ D E + F Sbjct: 383 IIRFAPPLVITEEQLHDCCDIIEKTIQNF 411 Lambda K H 0.321 0.137 0.412 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: 417 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: 406 Length of database: 413 Length adjustment: 31 Effective length of query: 375 Effective length of database: 382 Effective search space: 143250 Effective search space used: 143250 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