Align C4-dicarboxylate transporter, YhiT (characterized)
to candidate BWI76_RS01510 BWI76_RS01510 anaerobic C4-dicarboxylate transporter
Query= TCDB::Q8ZLD2 (439 letters) >FitnessBrowser__Koxy:BWI76_RS01510 Length = 446 Score = 334 bits (856), Expect = 4e-96 Identities = 171/444 (38%), Positives = 281/444 (63%), Gaps = 13/444 (2%) Query: 2 FWTELCFILVALMIGARIGGVFLGMVGGLGVGVMVFIFGLTPSTPPIDVILIILSVVLAA 61 F +L IL+ L GA+ GG+ LG++GG+G+ ++VF+F L P PP+DV+L+I++VV A+ Sbjct: 3 FAIQLIIILICLFYGAKKGGIALGLLGGIGLVILVFVFHLKPGKPPVDVMLVIIAVVAAS 62 Query: 62 ASLQASGGLDLLVKLAEKILRRHPRYITLLAPFICYIFTFMSGTGHVVYSLLPVISEVAR 121 A+LQASGGLD+++++AEK+LRR+P+Y++++APF+ T + GTGHVVY++LP+I +VA Sbjct: 63 ATLQASGGLDVMLQIAEKLLRRNPKYVSIVAPFVTCTLTILCGTGHVVYTILPIIYDVAI 122 Query: 122 DSGIRPERPLSISVIASQQAITASPISAAMAAMIGLMAPL-----GVSISTIMMICVPAT 176 + IRPERP++ S I +Q I ASP+S A+ +++ ++ + ++ I +P+T Sbjct: 123 KNNIRPERPMAASSIGAQMGIIASPVSVAVVSLVAMLGNFTFNGKHLEFLDLLAITIPST 182 Query: 177 LIGVAMGAIATFNKGKELKDDPEYQRRLAEGLIKPAQKESKNTVVTSRAK----LSVALF 232 L+G+ I ++ +GK+L DPE+Q +A + T++ + +++ +F Sbjct: 183 LLGILAIGIFSWFRGKDLDKDPEFQAFIAVPENRHYVYGDTATLLDKKLPTSNWIAMWIF 242 Query: 233 LTSAIVIVLLGLIPALRPMVETAKGLQPLSMSAAIQITMLSFACLIVLLCRPQVDQIISG 292 L S V+ LLG LRP+V+ + LSM IQ+ ML LI+++ + I Sbjct: 243 LASIAVVALLGAFSELRPVVDG----KALSMVLVIQMFMLLSGALIIIITKTNPASISKN 298 Query: 293 TVFRAGALAIVCAFGLAWMSETFVNGHIALIKAEVQTLLQQHTWLIAIMMFFVSAMVSSQ 352 VFR+G +AIV +G+AWM+ET H+ IK + +++++ W AI++ VS V+SQ Sbjct: 299 EVFRSGMIAIVAVYGIAWMAETMFGAHMTEIKGVLGEMVKEYPWAYAIVLLLVSKFVNSQ 358 Query: 353 AATTLILLPLGLALGLPAYALIGSWPAVNGYFFIPVAGQCLAALAFDDTGTTRIGKYVLN 412 AA ++P+ LA+G+ ++ S PA GY+ +P LAA+ FD +GTT IG++V+N Sbjct: 359 AAALAAIVPVALAIGVDPAYIVASAPACYGYYILPTYPSDLAAIQFDRSGTTHIGRFVIN 418 Query: 413 HSFMRPGLVNVIVSVIVGLLIGKM 436 HSF+ PGL+ V VS + G + M Sbjct: 419 HSFILPGLIGVSVSCVFGWVFAAM 442 Lambda K H 0.328 0.141 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: 417 Number of extensions: 23 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: 439 Length of database: 446 Length adjustment: 32 Effective length of query: 407 Effective length of database: 414 Effective search space: 168498 Effective search space used: 168498 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 51 (24.3 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