Align C4-dicarboxylate transporter, YhiT (characterized)
to candidate WP_017220705.1 A923_RS0105740 anaerobic C4-dicarboxylate transporter
Query= TCDB::Q8ZLD2 (439 letters) >NCBI__GCF_000276805.1:WP_017220705.1 Length = 442 Score = 371 bits (953), Expect = e-107 Identities = 189/444 (42%), Positives = 299/444 (67%), Gaps = 9/444 (2%) Query: 1 MFWTELCFILVALMIGARIGGVFLGMVGGLGVGVMVFIFGLTPSTPPIDVILIILSVVLA 60 M + E F+LV L IG+R GG+ LG+V G+G+ + VFIF + P++PP+ V+LIIL+VV Sbjct: 1 MLYFEFLFLLVVLYIGSRYGGIGLGVVSGIGLVIEVFIFKMPPTSPPVTVMLIILAVVTC 60 Query: 61 AASLQASGGLDLLVKLAEKILRRHPRYITLLAPFICYIFTFMSGTGHVVYSLLPVISEVA 120 A+ L+A+GGL ++++AE+ILR++P+ +T++APF+ Y TF+ GTGH VYS++P+I +VA Sbjct: 61 ASILEAAGGLKYMLQVAERILRKNPKRVTIIAPFVTYAMTFLLGTGHAVYSIMPIIGDVA 120 Query: 121 RDSGIRPERPLSISVIASQQAITASPISAAMAAMIGLMAPLGVSIS--TIMMICVPATLI 178 +GIRPERP++ + +ASQ AITASP+SAA+ + + + SI+ +I+M+ VP+TL Sbjct: 121 LKNGIRPERPMAAASVASQIAITASPLSAAVVFYLAQLVDIDSSITLLSILMVTVPSTLF 180 Query: 179 GVAMGAIATFNKGKELKDDPEYQRRLAEGL----IKPAQKESKNTVVTSRAKLSVALFLT 234 G M A+ + +GKEL DD EYQ RL + + I S + + ++A+ +V +FL Sbjct: 181 GTLMLALYSLRRGKELDDDEEYQARLKDPIWREKILNTTSTSLDEKLPTKARNAVLIFLG 240 Query: 235 SAIVIVLLGLIPALRPMVETAKGLQPLSMSAAIQITMLSFACLIVLLCRPQVDQIISGTV 294 + + IV++ + P +R + E G P+ MS IQ+ ML+F +I+L + + +G V Sbjct: 241 AILSIVVIAMFPEIRTITE---GAAPIKMSVVIQMMMLAFGGVILLATKTDPRDVPNGVV 297 Query: 295 FRAGALAIVCAFGLAWMSETFVNGHIALIKAEVQTLLQQHTWLIAIMMFFVSAMVSSQAA 354 F++G +A + FG+AWMS+T+ + +A + ++ H W A+ +F VS +V+SQAA Sbjct: 298 FKSGMVAAIAIFGIAWMSDTYFQYAMPQFRAGIVDMVTLHPWTFALALFIVSVVVNSQAA 357 Query: 355 TTLILLPLGLALGLPAYALIGSWPAVNGYFFIPVAGQCLAALAFDDTGTTRIGKYVLNHS 414 T ++LP+GLALGL +IG PAV GYFFIP +A + FD++GTT+IGKY NHS Sbjct: 358 TARMMLPVGLALGLEPALVIGLMPAVYGYFFIPNYPSDIATVNFDNSGTTKIGKYYFNHS 417 Query: 415 FMRPGLVNVIVSVIVGLLIGKMVL 438 FM GL+ V+ + +VG ++G++V+ Sbjct: 418 FMAVGLIGVVSACLVGYVLGQIVI 441 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: 385 Number of extensions: 15 Number of successful extensions: 3 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: 442 Length adjustment: 32 Effective length of query: 407 Effective length of database: 410 Effective search space: 166870 Effective search space used: 166870 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