Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate HSERO_RS23240 HSERO_RS23240 omega amino acid--pyruvate aminotransferase
Query= reanno::pseudo1_N1B4:Pf1N1B4_3440 (406 letters) >FitnessBrowser__HerbieS:HSERO_RS23240 Length = 442 Score = 152 bits (383), Expect = 2e-41 Identities = 121/409 (29%), Positives = 180/409 (44%), Gaps = 42/409 (10%) Query: 20 NYAPAAFIPVRGAGSRVWDQSGRELIDFAGGIAVNVLGHAHPALVAALTEQANKLWHVSN 79 N+ A + V G D +G ++D G+ LGHAHP +V+A+ + L + + Sbjct: 24 NFKAAPRMLVSAEGMHYRDDAGNTILDGTAGLWCVPLGHAHPKIVSAVQKSVATLDYAPS 83 Query: 80 VFTNEP-ALRLAHKLVDATFAE--RVFFCNSGAEANEAAFKLARRVAHDRFGTEKYEIVA 136 P A LA +L T VF+ SG+EA + A K+A + + ++ Sbjct: 84 FQLGHPSAFELAERLKAYTGNRFGNVFYTGSGSEAVDTALKIALAYHRAKGNATRTRLIG 143 Query: 137 ALNSFHGRTLFTVNVGGQSKYSDGFGPKIT-GITHVPYNDLAALKAAV------------ 183 +HG ++VGG F + G+ H+P+ A Sbjct: 144 RERGYHGVGFGGMSVGGIGGNRKTFSTALLPGVDHLPHTHNLEKNAFTKGEPEYGAHLAD 203 Query: 184 ----------SDKTCAVVLEPIQGEGGVLPAELSYLQGARELCDAHNALLVFDEVQTGMG 233 + AV++EP+ G GVL YL+ RE+C H LL+FDEV TG G Sbjct: 204 ELERLVTLHDASNIAAVIVEPVAGSTGVLIPPKGYLKRLREICTKHGILLIFDEVITGFG 263 Query: 234 RSGKLFAYQHYGVTPDILTSAKSLGGG-FPIAAMLTTEDLAKHLVVGT------HGTTYG 286 R G FA ++ V PDI T+AK L G P+ A+ ++ + G HG TY Sbjct: 264 RLGTPFASDYFDVEPDIFTTAKGLTNGVVPMGAVFVKPEIHDAFMNGPDGIELFHGYTYS 323 Query: 287 GNPLACAVAEAVIDVINTPEVLNGVNAKHDKFKTRLEQIGEKYGL--FTEVRGLGLLLGC 344 G+PLACA A ++V T VL A D F+ E GL +VR +GL+ G Sbjct: 324 GHPLACAAGLASLEVFQTEGVLENAQAVADYFQ---EAAHALRGLPHVIDVRTIGLIAGI 380 Query: 345 VLSD---AWKGKAKDIFNAAEREGLMILQAGPDVIRFAPSLVVEDADID 390 L+ +A D F A +G++I G D+I +P L++ ID Sbjct: 381 ELASIPGRVGARAYDAFVRAFNDGILIRVTG-DIIALSPPLIINKQQID 428 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: 443 Number of extensions: 24 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: 442 Length adjustment: 32 Effective length of query: 374 Effective length of database: 410 Effective search space: 153340 Effective search space used: 153340 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: 51 (24.3 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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