Align Sugar ABC transporter, periplasmic sugar-binding protein (characterized, see rationale)
to candidate WP_156804529.1 B3C1_RS10875 substrate-binding domain-containing protein
Query= uniprot:Q9WXW9 (335 letters) >NCBI__GCF_000299915.1:WP_156804529.1 Length = 309 Score = 82.4 bits (202), Expect = 1e-20 Identities = 82/271 (30%), Positives = 130/271 (47%), Gaps = 21/271 (7%) Query: 17 LVFLSVLLVAGL------SLALTIGVIGKSVHPYW-SQVEQGVKAAGKALGVDTKFFVPQ 69 ++ L L AGL +LA+T+G W S Q +K K+ G+D KF Q Sbjct: 1 MMTLKTLFAAGLMALSHSALAITVGFSQVGSESGWRSSFSQDMKDEAKSRGIDLKFADGQ 60 Query: 70 KEDINAQLQMLESFIAEGVNGIAIAPSDPTAVIPTIKKALEMGIPVVTLDTD-SPDSGRY 128 ++ N Q++ + SFIA+GV+ I IAP T P +K+A IPVV LD + G Y Sbjct: 61 QKQEN-QIRAVRSFIAQGVDAIIIAPVVETGWTPVLKEAKRARIPVVILDRNIKAAEGLY 119 Query: 129 V-YIGTDNYQAGYTAGLIMKELLGGKGKVVIGTGSLTAMNSLQRIQGFKDAI-KDSEIEI 186 V I +D + G A + + G+ +V G++ A ++ R +GF + I + +I Sbjct: 120 VTRIASDFTEEGRKAARWLMDKTKGQCNIVELQGTVGATAAIDRAKGFNEVIGAYPQAKI 179 Query: 187 VDILNDEEDGARAVSLAEAALNAHPDLDAFFGVYAYN-----GPAQALVVKNAG-KVGK- 239 V E A+ + E+ L A D + ++++N G QA +K AG K GK Sbjct: 180 VRSQTAEFTRAKGKEVMESFLKAE-DPQSLCALWSHNDEMALGAIQA--IKEAGLKPGKD 236 Query: 240 VKIVCFDTTPDILQYVKEGVIQATMGQRPYM 270 + +V D PD + + EG T+ P++ Sbjct: 237 LLVVSVDGVPDYFKAMAEGDANITVELNPHL 267 Lambda K H 0.318 0.137 0.388 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: 193 Number of extensions: 17 Number of successful extensions: 1 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: 335 Length of database: 309 Length adjustment: 28 Effective length of query: 307 Effective length of database: 281 Effective search space: 86267 Effective search space used: 86267 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 (21.7 bits) S2: 48 (23.1 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