Align ABC transporter substrate-binding protein (characterized, see rationale)
to candidate WP_086510099.1 BZY95_RS11690 ABC transporter substrate-binding protein
Query= uniprot:A0A166QFS3 (424 letters) >NCBI__GCF_002151265.1:WP_086510099.1 Length = 429 Score = 471 bits (1212), Expect = e-137 Identities = 231/417 (55%), Positives = 300/417 (71%), Gaps = 5/417 (1%) Query: 8 LPAALLTLCAGLPSLSSAADLTISCGAVGAELQLCKEAVQAWSKQTGNNVEVVSTPNSAT 67 L A+ LTL + + + AA +TI+CG G C E + W+++TG+ V VV+TP S T Sbjct: 18 LVASGLTL---VTTQAQAATITIACGD-GGSADFCPELARQWAQETGHEVAVVTTPQSGT 73 Query: 68 ERLSFYQQILSAQSSDIDIIQIDMVWPGMLAKHLLDLREVLPANATQGYFQAQVDNATVN 127 E LS YQQ+L ++SSDID++ +D VWPG+LA HL+DL + LP +A++G+F A +DN TV+ Sbjct: 74 ETLSLYQQLLGSKSSDIDVLMVDTVWPGLLAAHLIDLADYLPEDASEGFFPAMIDNNTVD 133 Query: 128 GRLVTMPWFTDSGLLYYRKDLLEKYNQQVPRTWEEMTATARNIQQAERTAGNPNAWGYIF 187 RL+ +PW++D+GLLYYR+DLLEKY+ VP TWE++T AR IQ AER AGN G++F Sbjct: 134 DRLLALPWYSDAGLLYYRRDLLEKYDHDVPETWEQLTEIAREIQNAEREAGNERMHGFVF 193 Query: 188 QGRAYEGLTCNALEWISSQPEGGLVNSRGDIVVNSQASRTALTLAKSWVGDISPRGVLNY 247 QGRAYEGLT NALEWI+S G +V+ G+I VN+ + ALTLA SWVGDI+PRGV NY Sbjct: 194 QGRAYEGLTTNALEWIASYGGGTIVDDDGNITVNNPQAAEALTLAASWVGDIAPRGVRNY 253 Query: 248 TEEEGRGVFQSGNALFMRNWPYVWALVQGQDSAVKDKVGVAPLPRGGETGTHASTLGGWG 307 EEE RG+FQSGNA+FMRNWPY WAL Q +A++ K GVAPLP G G +TLGGW Sbjct: 254 MEEEARGLFQSGNAVFMRNWPYAWALGQADGTAIQGKFGVAPLPH-GSAGESVATLGGWS 312 Query: 308 LAVSRYSAHPKLAAELVSYLTSAQEQKHRALIGAYNPVIESLYQDPELLAAMPYYAQLHS 367 AVSRYS +P LAAELV+YLT+ +QK A+ NP +LYQD E+L P+ +L+ Sbjct: 313 WAVSRYSKNPDLAAELVAYLTAEAQQKAHAIRFGMNPTRVTLYQDKEVLEVQPFIGELYD 372 Query: 368 ILNDGVMRPASITADRYPRVSNAFFDRVHGVLAGELPVDQALAELESELTRIKRRNW 424 L GV RPA++T + Y RVSNAFF+RVH VL+G+L +QAL +LE EL RI RR W Sbjct: 373 TLVSGVPRPANVTGEHYTRVSNAFFNRVHDVLSGDLTAEQALGQLERELNRISRRGW 429 Lambda K H 0.316 0.131 0.392 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: 507 Number of extensions: 14 Number of successful extensions: 2 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: 424 Length of database: 429 Length adjustment: 32 Effective length of query: 392 Effective length of database: 397 Effective search space: 155624 Effective search space used: 155624 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: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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