Align C4-dicarboxylate transporter, YhiT (characterized)
to candidate BWI76_RS05695 BWI76_RS05695 anaerobic C4-dicarboxylate transporter
Query= TCDB::Q8ZLD2 (439 letters) >FitnessBrowser__Koxy:BWI76_RS05695 Length = 429 Score = 238 bits (608), Expect = 2e-67 Identities = 135/435 (31%), Positives = 247/435 (56%), Gaps = 23/435 (5%) Query: 1 MFWTELCFILVALMIGARIGGVFLGMVGGLGVGVMVFIFGLTPSTPPIDVILIILSVVLA 60 M + +L+ L IG R+GG+ +G GG GV +++ G TP P+ VI+ I+ V++A Sbjct: 1 MILVQFLVVLLFLYIGMRVGGIGVGFAGGAGV-IVLSALGATPGDMPMLVIVFIMVVIVA 59 Query: 61 AASLQASGGLDLLVKLAEKILRRHPRYITLLAPFICYIFTFMSGTGHVVYSLLPVISEVA 120 A++Q +GG++ LV L E++LRR+PR + + AP ++ T M+ TG V ++ +PVI VA Sbjct: 60 IAAMQEAGGIEYLVDLTERLLRRYPRLLVITAPLSTWLLTMMASTGQVSFACMPVIVGVA 119 Query: 121 RDSGIRPERPLSISVIASQQAITASPISAAMAAMIGLMAP--LGVSISTIMMICVPATLI 178 +++ I+P R L++SV AS I ASPISAA+ G++ G ++ + +P+T + Sbjct: 120 KENNIKPTRALALSVSASLLGIVASPISAAVIFFSGILEKGHNGWGYIELIAVSIPSTFL 179 Query: 179 GVAMGAIATFNKGKELKDDPEYQRRLAEGLIKPAQKESKNTVVTSRAKLSVALFLTSAIV 238 + + + D Q RL + ++ V +R + ++ + +++ Sbjct: 180 ALLVTSFFYL-----FWDRIRQQDRLCDNPVQ----------VKARTERAIPPYAGRSVL 224 Query: 239 IVLLGLIPALRPMVETAKGL----QPLSMSAAIQI-TMLSFACLIVLLCRPQVDQIISGT 293 I ++GL+ L + T+ L P+ S ++ M+ A LIV+ CR V ++ SG+ Sbjct: 225 IFIVGLVAVLAYAIVTSPKLGLIAHPVMSSGQARVGVMMGVALLIVVCCRVNVHKVPSGS 284 Query: 294 VFRAGALAIVCAFGLAWMSETFVNGHIALIKAEVQTLLQQHTWLIAIMMFFVSAMVSSQA 353 VF+ G + +C G+AW+ TF++ + +++ V + L ++A+++ S + SQA Sbjct: 285 VFKTGMTSCICILGVAWLGSTFMDSNQQWLQSTVSSHLLDSPIMLALIIMAASCFLYSQA 344 Query: 354 ATTLILLPLGLALGLPAYALIGSWPAVNGYFFIPVAGQCLAALAFDDTGTTRIGKYVLNH 413 A+T IL P L++G+ L+ +PA F +P LAA+ DDTG+T++G+++++H Sbjct: 345 ASTKILFPAALSMGVAPAILVACFPATASLFILPNYPTLLAAVELDDTGSTKLGRHIIDH 404 Query: 414 SFMRPGLVNVIVSVI 428 F+ PGL +V++S++ Sbjct: 405 PFLLPGLASVLLSIL 419 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: 363 Number of extensions: 13 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: 439 Length of database: 429 Length adjustment: 32 Effective length of query: 407 Effective length of database: 397 Effective search space: 161579 Effective search space used: 161579 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