Align Citrate uptake transporter, membrane subunit, component of Pmf-dependent citrate uptake porter, TctABC (characterized)
to candidate Ac3H11_61 Tricarboxylate transport membrane protein TctA
Query= TCDB::S5Y5N9 (510 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_61 Length = 494 Score = 468 bits (1204), Expect = e-136 Identities = 231/496 (46%), Positives = 331/496 (66%), Gaps = 7/496 (1%) Query: 8 MEGFAGALTPMNLLWVIVGCLLGTAVGVMPGLGSSMAVALLLPMTFALDPTAAFIMFSGV 67 M+GFA A TP+NLLW VGC++GTAVGV+PG+G ++AVA+LLP+T ++ TA+ I F+G+ Sbjct: 1 MQGFATAATPINLLWAFVGCMIGTAVGVLPGIGPAVAVAMLLPITVKVEATASMIFFAGI 60 Query: 68 YFGGLFGDSTMAILMNTPGQASAIASTFEGHRMALNGRAPQALATAAIGAFIGGIVSSFI 127 Y+G ++G ST +IL+NTPG+A ++ + EG++MA NGRA ALATAAIG+F+ G +++ + Sbjct: 61 YYGAMYGGSTTSILLNTPGEAGSMVTAMEGNKMAKNGRAGAALATAAIGSFVAGTIATVL 120 Query: 128 VVFLAPTLAELSTAFGPAEYFALALFAFVATSSVVSDSVFKGLASLIFGLGIATIGIDSV 187 V F AP +AE + GP EYF L + AF S+V+ S +G+ +L GL + IGID + Sbjct: 121 VTFFAPLVAEYAVRLGPPEYFMLMVLAFTTVSAVLGKSTLRGMVALFVGLAMGLIGIDQL 180 Query: 188 TGIERFTLGAPQLFDGISLVTVTVAILALGEVFY-IAARARRDKANLETRSAGRPWLTGT 246 TG R+T G P+L DGI +V + V + A+GE Y + + D+ S +T Sbjct: 181 TGQARYTGGVPELMDGIEVVLIAVGLFAVGEALYNVMYEGKTDETQNRLTST---HMTKE 237 Query: 247 EFKEAAPAWARGTIIGLPFGVIPVGGSEVPTFLAYSTERALDKRRKDPQFGDKGAIRGLA 306 E+K + PAW R T IG PFG +P GGSE+PTFL+Y+ E+ L K ++ +FG GAI G+A Sbjct: 238 EWKRSWPAWLRATFIGFPFGTVPAGGSEIPTFLSYAAEKKLSKNKE--EFGTTGAIEGVA 295 Query: 307 APEAAGNATTGMAMGALLALGLPVSATAAIMLAAFRQYGIQPGPLLFDRNPELVWALLAS 366 PEAA NA + LL LG+P S T AI+L AF+ YGIQPGP LFD N LVWAL+AS Sbjct: 296 GPEAANNAAITATLIPLLTLGIPTSNTTAILLGAFQNYGIQPGPQLFDTNGALVWALIAS 355 Query: 367 FFIAMIVLLFINLPFAQLWAKLLLIPNHYLYSGIALFCGLGIYATSGAVFDLLMLLGIGV 426 +I ++LL +NLP LW KLL IP YLY+GI +F LG+Y + FDL++L IG+ Sbjct: 356 MYIGNVMLLILNLPLVGLWVKLLNIPKSYLYAGILVFSTLGVYGMRQSAFDLVLLYAIGL 415 Query: 427 VALIMRRYGYPLAPLMIGMVLGPLAETSLRDALLSSVGDFSILVSSPITWSLYA-VLAIF 485 + ++MRR+ +P AP+++GM+LGPLAE +R+A+ G ++I + P + +L VLA+ Sbjct: 416 LGVVMRRFDFPAAPVVVGMILGPLAEAQMRNAVAIGEGKWTIFLERPGSVTLIVIVLAVL 475 Query: 486 IAVSVITAIRGRRKHL 501 I ++ R+ L Sbjct: 476 IVPRLLRRWAARKMAL 491 Lambda K H 0.326 0.141 0.414 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: 751 Number of extensions: 38 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 510 Length of database: 494 Length adjustment: 34 Effective length of query: 476 Effective length of database: 460 Effective search space: 218960 Effective search space used: 218960 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 (21.6 bits) S2: 52 (24.6 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