Align GtsD (GLcK), component of Glucose porter, GtsABCD (characterized)
to candidate WP_086510784.1 BZY95_RS15425 ABC transporter ATP-binding protein
Query= TCDB::Q88P35 (384 letters) >NCBI__GCF_002151265.1:WP_086510784.1 Length = 373 Score = 372 bits (956), Expect = e-108 Identities = 207/377 (54%), Positives = 256/377 (67%), Gaps = 17/377 (4%) Query: 1 MATLELRNVNKTYGSGLPDTLKDIQLSIKDGEFLILVGPSGCGKSTLMNCIAGLEQITGG 60 MA LE+ NV K +GS LKD+ L+I GEFLILVGPSGCGKSTLMN IAGLE +T G Sbjct: 1 MAALEINNVCKDFGS--EQVLKDVSLAIDSGEFLILVGPSGCGKSTLMNAIAGLEPVTSG 58 Query: 61 AILIDEQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKLPQAAIDEEVARVA 120 I I + V+ +P +RDIAMVFQSYALYP+M+VR+NI FGL++RK+P+A + V RVA Sbjct: 59 EIRIAGESVTWQTPAERDIAMVFQSYALYPSMTVRQNISFGLEMRKVPKAEREAAVERVA 118 Query: 121 KLLQIEHLLARKPAQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 LLQI HLL RKP+QLSGGQ+QRVAMGRALAR PK+YLFDEPLSNLDAKLRV+MRTE+K Sbjct: 119 DLLQIGHLLERKPSQLSGGQRQRVAMGRALAREPKVYLFDEPLSNLDAKLRVDMRTEIKK 178 Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPQQIYNDPANQFVASFIGSPP 240 +HQRL TT VYVTHDQIEAMTL D +AVM+DG I Q G+P ++YNDP + FVA F+GSP Sbjct: 179 LHQRLGTTIVYVTHDQIEAMTLADCIAVMRDGRILQLGSPDEVYNDPVDLFVAGFMGSPS 238 Query: 241 MNFIPVRLARQDGRL-LALLDSGQARCELPLGE-----AADALEGREIILGIRPEQIA-- 292 MNFI L G L + G+ ELP + A G +ILG+RPE Sbjct: 239 MNFISATLVGGSGAYRLRVETPGEETLELPWPQERETPALGEKVGERVILGLRPEHFTED 298 Query: 293 ---LGA-ADGNGLPAIRAEVQVTEPTGPDLLVFVTLNQTKVCCRLAPDVACRVGDTLNLQ 348 LG A+G A+ + V EPTG D+L+ + L + R+ P + G+ L L+ Sbjct: 299 DARLGEYAEG---VALTPRITVVEPTGADILLQLKLGDGEATARVGPKCRVKAGERLTLR 355 Query: 349 FDPARVLLFDAANGERL 365 D R ++FD +RL Sbjct: 356 IDMGRAVMFDRETEKRL 372 Lambda K H 0.320 0.137 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: 448 Number of extensions: 15 Number of successful extensions: 4 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: 384 Length of database: 373 Length adjustment: 30 Effective length of query: 354 Effective length of database: 343 Effective search space: 121422 Effective search space used: 121422 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 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