Align C4-dicarboxylate transporter, YhiT (characterized)
to candidate 352283 BT2756 anaerobic C4-dicarboxylate transporter dcuB (NCBI ptt file)
Query= TCDB::Q8ZLD2 (439 letters) >FitnessBrowser__Btheta:352283 Length = 436 Score = 438 bits (1126), Expect = e-127 Identities = 215/428 (50%), Positives = 312/428 (72%) Query: 5 ELCFILVALMIGARIGGVFLGMVGGLGVGVMVFIFGLTPSTPPIDVILIILSVVLAAASL 64 +L F+L A++IGAR+GG+ LG++GG+G+G++ F+FGL P+ PPIDV+L+I +V+ AA+ + Sbjct: 4 QLAFVLTAIIIGARLGGIGLGVMGGVGLGILTFVFGLQPTAPPIDVMLMIAAVISAASCM 63 Query: 65 QASGGLDLLVKLAEKILRRHPRYITLLAPFICYIFTFMSGTGHVVYSLLPVISEVARDSG 124 QA+GGLD +VKLAE +LR++P ++TLL+P + Y+FTF++GTGHV YS+LPVI+EVA ++ Sbjct: 64 QAAGGLDYMVKLAEHLLRKNPSHVTLLSPLVTYLFTFIAGTGHVAYSVLPVIAEVATETK 123 Query: 125 IRPERPLSISVIASQQAITASPISAAMAAMIGLMAPLGVSISTIMMICVPATLIGVAMGA 184 IRPERPL I+VIASQQAITASPISAA A++GL+A +++ I+ I +PAT+IGV +GA Sbjct: 124 IRPERPLGIAVIASQQAITASPISAATVALLGLLAGFDITLFDILKITIPATIIGVLVGA 183 Query: 185 IATFNKGKELKDDPEYQRRLAEGLIKPAQKESKNTVVTSRAKLSVALFLTSAIVIVLLGL 244 + + GKEL +DPEYQ+RL EGL + E K+ A LSV +F+ + IVL G Sbjct: 184 LFSMKVGKELIEDPEYQKRLKEGLFNDKKIEIKDVKNKRSAMLSVLIFILATAFIVLFGS 243 Query: 245 IPALRPMVETAKGLQPLSMSAAIQITMLSFACLIVLLCRPQVDQIISGTVFRAGALAIVC 304 +RP + L MS+ I+I MLS A +I+++ + + G+VF AG A++ Sbjct: 244 FEGMRPSFLIDGEIVTLGMSSIIEIVMLSAAAIILIVTKTDGIKATQGSVFPAGMQAVIA 303 Query: 305 AFGLAWMSETFVNGHIALIKAEVQTLLQQHTWLIAIMMFFVSAMVSSQAATTLILLPLGL 364 FG+AWM +TF+ G++A + ++ +++Q WL I +F +S ++ SQAAT L+PLG+ Sbjct: 304 IFGIAWMGDTFLQGNMAQLTLSIEGIVRQMPWLFGIALFVMSILLYSQAATVRALMPLGI 363 Query: 365 ALGLPAYALIGSWPAVNGYFFIPVAGQCLAALAFDDTGTTRIGKYVLNHSFMRPGLVNVI 424 ALG+ Y LI +PAVNGYFFIP +AA+ FD TGTT+IGKYVLNHSFM PGLV+ + Sbjct: 364 ALGISPYMLIALFPAVNGYFFIPNYPTVVAAINFDRTGTTKIGKYVLNHSFMMPGLVSTV 423 Query: 425 VSVIVGLL 432 V++++GLL Sbjct: 424 VAIVLGLL 431 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: 398 Number of extensions: 10 Number of successful extensions: 1 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: 436 Length adjustment: 32 Effective length of query: 407 Effective length of database: 404 Effective search space: 164428 Effective search space used: 164428 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