Align C4-dicarboxylate transporter, YhiT (characterized)
to candidate BWI76_RS02325 BWI76_RS02325 anaerobic C4-dicarboxylate transporter
Query= TCDB::Q8ZLD2 (439 letters) >FitnessBrowser__Koxy:BWI76_RS02325 Length = 433 Score = 375 bits (963), Expect = e-108 Identities = 196/438 (44%), Positives = 285/438 (65%), Gaps = 5/438 (1%) Query: 1 MFWTELCFILVALMIGARIGGVFLGMVGGLGVGVMVFIFGLTPSTPPIDVILIILSVVLA 60 MF EL +L+A+ +GAR+GG+ +G GGLGV V+ +F + P P DVI II++V+ A Sbjct: 1 MFGAELVIVLLAIYLGARLGGIGIGFAGGLGVLVLTLVFQIKPGAIPFDVIEIIMAVIAA 60 Query: 61 AASLQASGGLDLLVKLAEKILRRHPRYITLLAPFICYIFTFMSGTGHVVYSLLPVISEVA 120 A++Q +GG+D LV LAE++LRRHP+YIT LAP + + T ++GTGH +S LPVI+EVA Sbjct: 61 IAAMQVAGGMDYLVSLAERMLRRHPKYITFLAPLVTWFMTVLAGTGHTAFSTLPVITEVA 120 Query: 121 RDSGIRPERPLSISVIASQQAITASPISAAMAAMIGLMAPLGVSISTIMMICVPATLIGV 180 ++ GIRP RPLSI+V+ASQ AITASPISAA+ G++ PLGVS T++ IC+P TLI V Sbjct: 121 KEQGIRPSRPLSIAVVASQIAITASPISAAVVFFAGILEPLGVSYLTLLAICIPVTLIAV 180 Query: 181 AMGAIATFNKGKELKDDPEYQRRLAEGLIKPAQKESKNTVVTSRAKLSVALFLTSAIVIV 240 + AI G ELKDDP YQ RLA+G +K + S+ + A+ SV LFL I ++ Sbjct: 181 MLTAIVCNFLGCELKDDPIYQERLAKGEVK--LRGSQVFELKPHARRSVLLFLIGIIAVM 238 Query: 241 LLGLIPALRPMVETAKGLQPLSMSAAIQITMLSFACLIVLLCRPQVDQIISGTVFRAGAL 300 A+ V + L + AI + ML+ A LI + C+ ++++ + F++G Sbjct: 239 FYA--TAISDTVGLIQN-PVLPRNEAIVVFMLTIATLISITCKIDTGEVLNASTFKSGMS 295 Query: 301 AIVCAFGLAWMSETFVNGHIALIKAEVQTLLQQHTWLIAIMMFFVSAMVSSQAATTLILL 360 A VC G+AW+ +TFV HI+ I+ LL + WL+A+++FF + ++ SQAATT L+ Sbjct: 296 ACVCVLGVAWLGDTFVKAHISDIQTVAGDLLHNYPWLLAVVLFFAATLLYSQAATTKALM 355 Query: 361 PLGLALGLPAYALIGSWPAVNGYFFIPVAGQCLAALAFDDTGTTRIGKYVLNHSFMRPGL 420 P L LG+ I S+ AV+ F +P LAA+ DDTG+TRIGKYV NH+F+ PG+ Sbjct: 356 PAALMLGVSPLTAIASFAAVSALFVLPTYPTLLAAVEMDDTGSTRIGKYVFNHAFLIPGV 415 Query: 421 VNVIVSVIVGLLIGKMVL 438 + + + VI+G + G ++L Sbjct: 416 IAITLCVILGFIFGGIML 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: 406 Number of extensions: 19 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 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