Align C4-dicarboxylate transporter, YhiT (characterized)
to candidate WP_017220126.1 A923_RS0102800 anaerobic C4-dicarboxylate transporter
Query= TCDB::Q8ZLD2 (439 letters) >NCBI__GCF_000276805.1:WP_017220126.1 Length = 433 Score = 357 bits (915), Expect = e-103 Identities = 189/441 (42%), Positives = 275/441 (62%), Gaps = 11/441 (2%) Query: 1 MFWTELCFILVALMIGARIGGVFLGMVGGLGVGVMVFIFGLTPSTPPIDVILIILSVVLA 60 M +L +L+ + +GARIGG+ +G GG GV V+ I GL + PIDVILII+SV+ A Sbjct: 1 MIVVQLFVVLLFIYLGARIGGIGIGFAGGAGVLVLTMILGLDAGSIPIDVILIIMSVITA 60 Query: 61 AASLQASGGLDLLVKLAEKILRRHPRYITLLAPFICYIFTFMSGTGHVVYSLLPVISEVA 120 A++Q +GG+D LV LAEK LR++P+ IT AP + Y T ++GTGH +S LPVI+EVA Sbjct: 61 IAAMQVAGGMDWLVDLAEKFLRKNPKRITFYAPIVTYFMTVLAGTGHTAFSTLPVIAEVA 120 Query: 121 RDSGIRPERPLSISVIASQQAITASPISAAMAAMIGLMAPLGVSISTIMMICVPATLIGV 180 ++ GIRP RPLSI+V+ASQ AITASPISAA+ G++ PLGV +++ +C+P+T + Sbjct: 121 KEQGIRPSRPLSIAVVASQIAITASPISAAVVFFSGILEPLGVDYLSLLAVCIPSTFLAC 180 Query: 181 AMGAIATFNKGKELKDDPEYQRRLAEGLIKPAQKESKNTVVTSRAKLSVALFLTSAIVIV 240 +GA G ELKDDP YQ RLA+GLIK + ++ + T AK SV +F + + +V Sbjct: 181 MVGAFVANYLGCELKDDPVYQDRLAKGLIKMNGEGKRDILPT--AKTSVYIFCAAIVAVV 238 Query: 241 LLGLIPALRPMVETAKGL---QPLSMSAAIQITMLSFACLIVLLCRPQVDQIISGTVFRA 297 A M+ + GL + + AI ML+ A IV + QI + F++ Sbjct: 239 ------AYATMISGSVGLIENPTIGRNEAIMALMLTAAACIVSFTKIDASQIANAATFKS 292 Query: 298 GALAIVCAFGLAWMSETFVNGHIALIKAEVQTLLQQHTWLIAIMMFFVSAMVSSQAATTL 357 G A VC G+AW+ +TFV+ HI IK ++L+Q+ W++A+++FF S ++ SQ ATT Sbjct: 293 GMSACVCVLGVAWLGDTFVSAHIGDIKEFSASILEQYPWMLAVVLFFASMLLYSQGATTT 352 Query: 358 ILLPLGLALGLPAYALIGSWPAVNGYFFIPVAGQCLAALAFDDTGTTRIGKYVLNHSFMR 417 L+P LA+G+ + S+ AV+ F +P LAA+ DDTG+TRIG V NH F Sbjct: 353 ALMPAALAIGVAPITAVASFAAVSALFVLPTYPTLLAAVEMDDTGSTRIGNLVFNHPFFI 412 Query: 418 PGLVNVIVSVIVGLLIGKMVL 438 PG+ + SV +G + G ++L Sbjct: 413 PGVATISTSVALGFVFGGLIL 433 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: 391 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: 433 Length adjustment: 32 Effective length of query: 407 Effective length of database: 401 Effective search space: 163207 Effective search space used: 163207 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 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