Align Extracellular solute-binding protein, family 3 (characterized, see rationale)
to candidate AZOBR_RS00530 AZOBR_RS00530 putative amino-acid ABC transporter substrate-binding protein
Query= uniprot:Q31RP1 (359 letters) >FitnessBrowser__azobra:AZOBR_RS00530 Length = 349 Score = 241 bits (615), Expect = 2e-68 Identities = 136/340 (40%), Positives = 198/340 (58%), Gaps = 8/340 (2%) Query: 21 VLLCFLPLAACRSLGGNETESNSRLNQVQARGKLLCGVEGRLPGFSFLDSQGNYSGLDVD 80 V+ L A GG E+ + V+ RG L CGV G + +D GN+ G VD Sbjct: 12 VVAAVLAAAVSAPSGGPRAET---MEDVRERGLLRCGVSSSGAGLAAVDDSGNWRGFFVD 68 Query: 81 ICKAIAAALFNDPKAIEYRSLDSVERFPALASGEVDLLSRNTTWTLSRDAKGGNNLEFAP 140 +C+A+AAA+ +E+ +S RF L +GEVD++ TTWTL RDA G ++F Sbjct: 69 MCRALAAAVAGKADRVEFVETNSENRFAILRNGEVDVVMEGTTWTLQRDATFG--IDFPA 126 Query: 141 TTFYDGQGLMVRRNSGIQSLQDFQ-GKSICVETGTTSELNLADTMRELGVQYQEIKFPNS 199 +DGQG + R G+ L D G S+CV TT+ NL D M GV+++ + ++ Sbjct: 127 VYLFDGQGFIAHRAHGVARLSDLPPGASVCVIEQTTTLRNLEDWMARTGVRFRLKRVRST 186 Query: 200 DANYAAYAQGRCEGVTSDRSQLAARRTTLS-DADQHQLLDAVISKEPLSPATLNNDSPWF 258 + +A+ C+ TSDR L A+R + + D + +L ISKEPL P ++ WF Sbjct: 187 EGALSAFFNHHCDLYTSDRIGLHAQRLLKAPERDDYVILPEAISKEPLGPMVRPDERRWF 246 Query: 259 DVVKWVVNATIQAEEFGITQANIDQFKT-SKNPEIRRFLGLEGELGQQLGLSNDFAYRAI 317 D+V+WV AT+ AEE GIT AN + K +++PE+RR LG +G LGL +D+A+R I Sbjct: 247 DIVRWVFLATVLAEEKGITAANAPRLKEEAQDPEVRRLLGATTGVGWGLGLDDDWAFRVI 306 Query: 318 KAVGNYGEIYERNVGQQSPLKLNRGLNQLYKNGGLLYSPP 357 VGNYGEI++R++G SPL ++RG+N L+ NGGL Y+PP Sbjct: 307 TQVGNYGEIFDRHLGAASPLGIDRGMNGLWMNGGLHYAPP 346 Lambda K H 0.317 0.134 0.391 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: 252 Number of extensions: 15 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: 359 Length of database: 349 Length adjustment: 29 Effective length of query: 330 Effective length of database: 320 Effective search space: 105600 Effective search space used: 105600 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 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