Align 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate CCNA_00620 CCNA_00620 acetylornithine aminotransferase/succinyldiaminopimelate aminotransferase
Query= BRENDA::Q0K2K2 (423 letters) >FitnessBrowser__Caulo:CCNA_00620 Length = 392 Score = 199 bits (505), Expect = 2e-55 Identities = 145/402 (36%), Positives = 194/402 (48%), Gaps = 46/402 (11%) Query: 30 RAENATLWDVEGRAYTDFAAGIAVLNTGHRHPRVMQAIAAQLERFTHTA--YQIVPYQGY 87 R E L+D +GR Y D AAG+AV GH PR++QA+ Q + H + Y++ + Sbjct: 17 RGEGCWLYDQDGRDYLDLAAGVAVNTLGHGDPRLVQALKTQADILWHASNLYRLPAQEAL 76 Query: 88 VTLAERINALVPIQGLNKTALFTTGAEAVENAIKIARAHTGRPG------VIAFSGAFHG 141 T L ++ +GAEAVE AIK AR G G V+ F AFHG Sbjct: 77 AT------KLTDATFADRVFFANSGAEAVEAAIKTARRWQGAKGRPERYRVLTFGNAFHG 130 Query: 142 RTLLGMALTGKVAPYKIGFGPFPSDIYHAPFPSALHGVSTERALQALEGLFKTDIDPARV 201 RTL ++ T ++ + GF P PF +EG + I P + Sbjct: 131 RTLATISATDQMK-VREGFTPLYDAFDTTPFND-------------IEGAARA-ITP-QT 174 Query: 202 AAIIVEPVQGEGGFQAAPADFMRGLRAVCDQHGIVLIADEVQTGFGRTGKMFAMSHHDVE 261 AAI+VEP+QGEGG A F+ GLRA+CDQH ++LI DEVQTG GRTG +FA + V Sbjct: 175 AAILVEPIQGEGGLTPATPGFLAGLRALCDQHDLLLILDEVQTGIGRTGHLFAHELYGVR 234 Query: 262 PDLITMAKSLAGGMPLSAVSGRAAIMDAPLPGGLGGTYAGNPLAVAAAHAVIDVIEEEKL 321 PD+I +AK L GG P+ A PG G TY GNPLA A A AV+D + Sbjct: 235 PDIIAVAKGLGGGFPIGACLATEDAASGMTPGSHGSTYGGNPLACAVASAVLDAVLAPGF 294 Query: 322 CE---RSASLGQQLREHLLAQRKHCPAMAEVRGLGSMVAAEFCDPATGQPSAEHAKRVQT 378 E A+L L E LL R+H +G G M G A+ V Sbjct: 295 LETVRERAALVDALLERLL--RRHSDLFVRAQGHGLM---------RGLQVRASARDVVA 343 Query: 379 RALEAGLVLLTCGTYGNVIRFLYPLTIPQAQFDAALAVLTQA 420 + G++ + G +V+R L PLTI + + A A L +A Sbjct: 344 HLRDFGVMTVAAG--ADVVRLLPPLTISELEIAEAEARLLRA 383 Lambda K H 0.321 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: 442 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: 423 Length of database: 392 Length adjustment: 31 Effective length of query: 392 Effective length of database: 361 Effective search space: 141512 Effective search space used: 141512 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 (21.9 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