Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate Echvi_0577 Echvi_0577 ornithine aminotransferase
Query= reanno::azobra:AZOBR_RS19025 (389 letters) >FitnessBrowser__Cola:Echvi_0577 Length = 413 Score = 221 bits (564), Expect = 2e-62 Identities = 132/386 (34%), Positives = 201/386 (52%), Gaps = 11/386 (2%) Query: 9 YARADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWHTSNL 68 Y +V RGEG +++ +G ++ DF + + GH +P +++ L QA L TS Sbjct: 23 YHPLPVVLSRGEGVFMWDVEGEKYYDFLSSYSAVNQGHCHPRILQTLIDQAGTLTLTSRA 82 Query: 69 FRVAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKARTR--IITFE 126 F K LTE D V N+GAE E K+ RK+ YEK II + Sbjct: 83 FHNDVLGPFEKFLTEYFGYDKVLPMNTGAEGVETAIKIARKWGYEKKGIPENEGTIIVAK 142 Query: 127 QAFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVRNAVTDET--AGICLEPIQ 184 FHGRT +S + E K FGP GF +P D++A+++ ++ G +EPIQ Sbjct: 143 NNFHGRTTTVISFSNDETARKNFGPYTPGFVTIPHDDIDALKDVLSQSKNIIGYLVEPIQ 202 Query: 185 GEGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDVMAVAKG 244 GE G+ +L+ + +C +HG+L DEIQ G+ RTGKL A + G+ PD++ + K Sbjct: 203 GEAGVYVPKEGYLKEVAAVCKDHGVLFMADEIQTGIARTGKLLACDHEGVKPDMLILGKA 262 Query: 245 IGGGF-PLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQRIG 303 I GGF P+ A LA + + G HGST+GGNPL V L+ V + ++ ++G Sbjct: 263 ISGGFYPVSAVLADDHIMEVIQPGQHGSTFGGNPLGAKVAMTALNVVKDEKLAENADKLG 322 Query: 304 GLLQDRLAGLVAENPAVFKGVRGKGLMLGLACGPAVGD-----VVVALRANGLLSVPAGD 358 L ++R+ LV ++ V + VRGKGL+ + + +AL+ NGLL+ P Sbjct: 323 KLFRERIQQLVDKSDLV-ELVRGKGLLNAIVINDTEDSDTAWRLCLALKENGLLAKPTHG 381 Query: 359 NVVRLLPPLNIGEAEVEEAVAILAKT 384 N++R PPL I E ++ + I+ KT Sbjct: 382 NIIRFAPPLVITEEQLHDCCDIIEKT 407 Lambda K H 0.321 0.139 0.414 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: 407 Number of extensions: 24 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: 389 Length of database: 413 Length adjustment: 31 Effective length of query: 358 Effective length of database: 382 Effective search space: 136756 Effective search space used: 136756 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