Align C4-dicarboxylate transporter, YhiT (characterized)
to candidate 18151 b4123 C4-dicarboxylate antiporter (NCBI)
Query= TCDB::Q8ZLD2 (439 letters) >FitnessBrowser__Keio:18151 Length = 446 Score = 333 bits (854), Expect = 6e-96 Identities = 172/445 (38%), Positives = 284/445 (63%), Gaps = 13/445 (2%) Query: 1 MFWTELCFILVALMIGARIGGVFLGMVGGLGVGVMVFIFGLTPSTPPIDVILIILSVVLA 60 +F +L IL+ L GAR GG+ LG++GG+G+ ++VF+F L P PP+DV+L+I++VV A Sbjct: 2 LFTIQLIIILICLFYGARKGGIALGLLGGIGLVILVFVFHLQPGKPPVDVMLVIIAVVAA 61 Query: 61 AASLQASGGLDLLVKLAEKILRRHPRYITLLAPFICYIFTFMSGTGHVVYSLLPVISEVA 120 +A+LQASGGLD+++++AEK+LRR+P+Y++++APF+ T + GTGHVVY++LP+I +VA Sbjct: 62 SATLQASGGLDVMLQIAEKLLRRNPKYVSIVAPFVTCTLTILCGTGHVVYTILPIIYDVA 121 Query: 121 RDSGIRPERPLSISVIASQQAITASPISAAMAAMIGLMAPL-----GVSISTIMMICVPA 175 + IRPERP++ S I +Q I ASP+S A+ +++ ++ + + ++ I +P+ Sbjct: 122 IKNNIRPERPMAASSIGAQMGIIASPVSVAVVSLVAMLGNVTFDGRHLEFLDLLAITIPS 181 Query: 176 TLIGVAMGAIATFNKGKELKDDPEYQRRLAEGLIKPAQKESKNTVVTSRAK----LSVAL 231 TLIG+ I ++ +GK+L D E+Q+ ++ + T++ + L++ + Sbjct: 182 TLIGILAIGIFSWFRGKDLDKDEEFQKFISVPENREYVYGDTATLLDKKLPKSNWLAMWI 241 Query: 232 FLTSAIVIVLLGLIPALRPMVETAKGLQPLSMSAAIQITMLSFACLIVLLCRPQVDQIIS 291 FL + V+ LLG LRP + G +PLSM IQ+ ML LI++L + I Sbjct: 242 FLGAIAVVALLGADSDLRP----SFGGKPLSMVLVIQMFMLLTGALIIILTKTNPASISK 297 Query: 292 GTVFRAGALAIVCAFGLAWMSETFVNGHIALIKAEVQTLLQQHTWLIAIMMFFVSAMVSS 351 VFR+G +AIV +G+AWM+ET H++ I+ + +++++ W AI++ VS V+S Sbjct: 298 NEVFRSGMIAIVAVYGIAWMAETMFGAHMSEIQGVLGEMVKEYPWAYAIVLLLVSKFVNS 357 Query: 352 QAATTLILLPLGLALGLPAYALIGSWPAVNGYFFIPVAGQCLAALAFDDTGTTRIGKYVL 411 QAA ++P+ LA+G+ ++ S PA GY+ +P LAA+ FD +GTT IG++V+ Sbjct: 358 QAAALAAIVPVALAIGVDPAYIVASAPACYGYYILPTYPSDLAAIQFDRSGTTHIGRFVI 417 Query: 412 NHSFMRPGLVNVIVSVIVGLLIGKM 436 NHSF+ PGL+ V VS + G + M Sbjct: 418 NHSFILPGLIGVSVSCVFGWIFAAM 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: 415 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