Align C4-dicarboxylate transporter, YhiT (characterized)
to candidate 18165 b4138 C4-dicarboxylate antiporter (NCBI)
Query= TCDB::Q8ZLD2 (439 letters) >FitnessBrowser__Keio:18165 Length = 433 Score = 343 bits (880), Expect = 6e-99 Identities = 184/445 (41%), Positives = 280/445 (62%), Gaps = 19/445 (4%) Query: 1 MFWTELCFILVALMIGARIGGVFLGMVGGLGVGVMVFIFGLTPSTPPIDVILIILSVVLA 60 M EL +L+A+ +GAR+GG+ +G GGLGV V+ I G+ P P DVI II++V+ A Sbjct: 1 MLVVELIIVLLAIFLGARLGGIGIGFAGGLGVLVLAAI-GVKPGNIPFDVISIIMAVIAA 59 Query: 61 AASLQASGGLDLLVKLAEKILRRHPRYITLLAPFICYIFTFMSGTGHVVYSLLPVISEVA 120 +++Q +GGLD LV EK+LRR+P+YIT+LAP + Y T +GTG++ + LPVI+EVA Sbjct: 60 ISAMQVAGGLDYLVHQTEKLLRRNPKYITILAPIVTYFLTIFAGTGNISLATLPVIAEVA 119 Query: 121 RDSGIRPERPLSISVIASQQAITASPISAAMAAMIGLMAPLGVSISTIMMICVPATLIGV 180 ++ G++P RPLS +V+++Q AITASPISAA+ M +M G+S ++ + +P+TL+ V Sbjct: 120 KEQGVKPCRPLSTAVVSAQIAITASPISAAVVYMSSVMEGHGISYLHLLSVVIPSTLLAV 179 Query: 181 -AMGAIATFNKGKELKDDPEYQRRLAEGLIKPAQKESKNTVVTSRAKLSVALFLTSAIVI 239 M + T +L DDP Y++RL EGL++ + K + S AK SV LFL + + Sbjct: 180 LVMSFLVTMLFNSKLSDDPIYRKRLEEGLVE--LRGEKQIEIKSGAKTSVWLFLLGVVGV 237 Query: 240 VLLGLI--PAL----RPMVETAKGLQPLSMSAAIQITMLSFACLIVLLCRPQVDQIISGT 293 V+ +I P++ +P++ T AI I MLS A L ++C+ D I++ + Sbjct: 238 VIYAIINSPSMGLVEKPLMNTTN---------AILIIMLSVATLTTVICKVDTDNILNSS 288 Query: 294 VFRAGALAIVCAFGLAWMSETFVNGHIALIKAEVQTLLQQHTWLIAIMMFFVSAMVSSQA 353 F+AG A +C G+AW+ +TFV+ +I IK ++Q H WL+A++ FF SA++ SQA Sbjct: 289 TFKAGMSACICILGVAWLGDTFVSNNIDWIKDTAGEVIQGHPWLLAVIFFFASALLYSQA 348 Query: 354 ATTLILLPLGLALGLPAYALIGSWPAVNGYFFIPVAGQCLAALAFDDTGTTRIGKYVLNH 413 AT L+P+ LAL + + S+ AV+G F +P +AA+ DDTGTTRIGK+V NH Sbjct: 349 ATAKALMPMALALNVSPLTAVASFAAVSGLFILPTYPTLVAAVQMDDTGTTRIGKFVFNH 408 Query: 414 SFMRPGLVNVIVSVIVGLLIGKMVL 438 F PG + V ++V G ++G +L Sbjct: 409 PFFIPGTLGVALAVCFGFVLGSFML 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: 410 Number of extensions: 18 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: 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 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