Align GlpV, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate AZOBR_RS25900 AZOBR_RS25900 ABC transporter substrate-binding protein
Query= TCDB::G3LHZ3 (569 letters) >FitnessBrowser__azobra:AZOBR_RS25900 Length = 584 Score = 872 bits (2252), Expect = 0.0 Identities = 418/567 (73%), Positives = 477/567 (84%), Gaps = 4/567 (0%) Query: 2 TTTAGLLLAMTASAYAGMDEAKTFLDKEVGDLSTLPRADQEKEMQWFVDAAKPFAGMDIK 61 + +A LL +A A+A ++ AK ++D E STL + DQ KEMQWF+DAAKPFAGM+I Sbjct: 8 SASAAALLLSSAPAFADIEAAKRWIDSEFQP-STLSKEDQLKEMQWFIDAAKPFAGMEIN 66 Query: 62 VVSETITTHEYESKVLAPAFTAITGIKITHDLIGEGDVVEKLQTQMQSGENIYDAYINDS 121 VVSETITTHEYE++ LA AF+ ITGIK+ HDLI EGDVVEK+QTQMQSG+NIYDA+INDS Sbjct: 67 VVSETITTHEYEARTLARAFSEITGIKLRHDLIQEGDVVEKIQTQMQSGKNIYDAWINDS 126 Query: 122 DLIGTHWRYQQARSLTDWMANEGKDVTNPGLDIDDFIGKSFTTAPDGKLYQLPDQQFANL 181 DLIGTH+RY+Q LTDWM EGKDVT P LD+ DFIG SFTTAPDGKLYQLPDQQFANL Sbjct: 127 DLIGTHFRYKQVVPLTDWMDGEGKDVTLPTLDVKDFIGTSFTTAPDGKLYQLPDQQFANL 186 Query: 182 YWFRYDWFNDEKNKADFKAKYGYDLGVPVNWSAYEDIAEFFTG--REIDGKKVFGHMDYG 239 YWFRYDWF + KA FKAKYGYDLGVPVNWSAYEDIAEFFT +EIDG KV+GHMDYG Sbjct: 187 YWFRYDWFTNPDIKAKFKAKYGYDLGVPVNWSAYEDIAEFFTNDVKEIDGVKVYGHMDYG 246 Query: 240 KKDPSLGWRFTDAWLSMAGNGDKGIPNGKPVDEWGIKVDENSRPVGSCVARGGDTNGPAA 299 KKDPSLGWRFTDAWLSMAGNGDKG+PNGKPVDEWGI++ E PVGS + RGGDTNGPAA Sbjct: 247 KKDPSLGWRFTDAWLSMAGNGDKGLPNGKPVDEWGIRM-EGCSPVGSSIERGGDTNGPAA 305 Query: 300 VYSIQKYLDWMKAYAPAAAQGMTFSESGPVPSQGEVAQQMFTYTAFTADFVKEGLPVVNA 359 VYS+ KY++W+K YAP A GMTFSESGPVP+QG VAQQMF YTAFTAD VK+GLPVVNA Sbjct: 306 VYSVTKYVEWLKKYAPPQAAGMTFSESGPVPAQGNVAQQMFWYTAFTADMVKDGLPVVNA 365 Query: 360 DGTPKWRFAPSPHGVYWKDGMKLGYQDAGSWTLMKSTPDDRAKAAWLYAQFVTSKTVDVK 419 DGTPKWR APSP G YWKDGMKLGYQDAGSWTL+KSTP DR KAAWLYAQF SK+V +K Sbjct: 366 DGTPKWRMAPSPKGAYWKDGMKLGYQDAGSWTLLKSTPVDRRKAAWLYAQFTMSKSVSLK 425 Query: 420 KSHMGLTFIRQSTLDHKSFTDRAPKLGGLIEFYRSPARLQWSPTGTNVPDYPKLAQLWWQ 479 KSH+GLTFIR+S + KSFT+RAPKLGGL+EFYRSPAR+QW+PTG NVPDYPKLAQLWWQ Sbjct: 426 KSHVGLTFIRESDIWDKSFTERAPKLGGLVEFYRSPARVQWTPTGVNVPDYPKLAQLWWQ 485 Query: 480 AIGDASSGAKTAQEAMDSLCSEQEKVLQRLERAKVQGDIGPKLAEEHDLAYWNADAVKNG 539 IGDASSGAKT Q AMD+L + Q+ V++RLER+ VQG+ GPKL ++ +W A A K+G Sbjct: 486 NIGDASSGAKTPQAAMDALAAAQDSVMERLERSGVQGECGPKLNKKESAEFWFAKAEKDG 545 Query: 540 NLAPQLKIENEKDKPVTVNYDELVKSW 566 APQ K+ NEK K TV+YD+L+KSW Sbjct: 546 TTAPQRKLSNEKPKGETVDYDQLIKSW 572 Lambda K H 0.315 0.132 0.409 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: 1349 Number of extensions: 53 Number of successful extensions: 3 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: 569 Length of database: 584 Length adjustment: 36 Effective length of query: 533 Effective length of database: 548 Effective search space: 292084 Effective search space used: 292084 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 (21.5 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Apr 09 2024. 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