Align Gluconolactonase (characterized, see rationale)
to candidate SMa0717 SMa0717 hypothetical protein
Query= uniprot:A0A165IRV8 (316 letters) >FitnessBrowser__Smeli:SMa0717 Length = 569 Score = 200 bits (509), Expect = 6e-56 Identities = 116/292 (39%), Positives = 154/292 (52%), Gaps = 7/292 (2%) Query: 25 VRCVIALGNALGEGVLWSVREQAVYWVDILGRELHRWDPATGAHQRWTFDEEISAIAERA 84 V+CV+ G LGE +W RE+ +YWVDIL +HR+DP TG ++ + +SA+ Sbjct: 283 VQCVLPWGAQLGEAPVWVEREKRLYWVDILHPAVHRFDPVTGKNESCNVAKLVSAVLPTR 342 Query: 85 HAPGFIVTLRRGFALFD-PATDMAPRYLHQPEPDRAGNRFNDGKCDAQGRFWAGSMDFAC 143 + G IV + G FD D P +PEP NR ND K D GR W GSM Sbjct: 343 NE-GLIVASQDGVEHFDFDRGDFNP--FAEPEPGLPENRLNDAKVDPSGRLWVGSMRLDV 399 Query: 144 EAPTGALYRYDSDGSCTRHDDGFAVTNGPTWSGTGQGAAMFFNATIEGNTYRYDSDLATG 203 PTG+LYR S G TR GF V NG WS + +F T+ G Y YD D G Sbjct: 400 SRPTGSLYRLTSAGEVTRAGSGFTVANGLAWS--PDSSTFYFVDTVPGIIYAYDFDAREG 457 Query: 204 TVSNKTLWKHWLPEDGLPDGMTTDAQGRLWIAHWGGWCVTCHDPVTAAELGRVRLPVSQV 263 +++N+ ++ +G PDG+ DA G +W A W GW V + P + V LPV + Sbjct: 458 SIANRRVFVTVPEAEGRPDGLAVDADGGVWCAIWDGWRVNRYRPDGRLDRA-VELPVPRP 516 Query: 264 TTCAFGGADLRTLFISSARVGLTPEQLAAEPLAGALFAVDTDSLGLPAHPFG 315 T+ AFGG +L TLFI+SAR L L PL+G +FA + + GLP FG Sbjct: 517 TSVAFGGDELATLFITSARTRLPASTLTEAPLSGGIFACNPGARGLPTSLFG 568 Lambda K H 0.321 0.137 0.457 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: 609 Number of extensions: 35 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: 316 Length of database: 569 Length adjustment: 32 Effective length of query: 284 Effective length of database: 537 Effective search space: 152508 Effective search space used: 152508 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 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