Align Citrate uptake transporter, membrane subunit, component of Pmf-dependent citrate uptake porter, TctABC (characterized)
to candidate PfGW456L13_3733 Tricarboxylate transport membrane protein TctA
Query= TCDB::S5Y5N9 (510 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3733 Length = 502 Score = 487 bits (1254), Expect = e-142 Identities = 240/501 (47%), Positives = 346/501 (69%), Gaps = 3/501 (0%) Query: 1 MDILSLLMEGFAGALTPMNLLWVIVGCLLGTAVGVMPGLGSSMAVALLLPMTFALDPTAA 60 +DILS L GF+ ALTP+NL+W +GCLLGTA+GV+PG+G ++ VALLLP+T +DPT A Sbjct: 1 VDILSSLAMGFSSALTPINLMWGFIGCLLGTAIGVLPGIGPALTVALLLPITAKVDPTGA 60 Query: 61 FIMFSGVYFGGLFGDSTMAILMNTPGQASAIASTFEGHRMALNGRAPQALATAAIGAFIG 120 IMF+G+Y+G FG ST +IL+NTPG++S++ + EG+ MA NGRA ALATAAIG+F+ Sbjct: 61 LIMFAGIYYGAQFGGSTTSILLNTPGESSSMVTALEGNLMARNGRAGPALATAAIGSFVA 120 Query: 121 GIVSSFIVVFLAPTLAELSTAFGPAEYFALALFAFVATSSVVSDSVFKGLASLIFGLGIA 180 G +++ ++ AP +A L+ FGP EYFA+ + +F S+V+ S+ +G ASL GL I Sbjct: 121 GTIATVLLTLFAPVVARLALNFGPTEYFAILVLSFTTVSAVLGASMLRGFASLGVGLTIG 180 Query: 181 TIGIDSVTGIERFTLGAPQLFDGISLVTVTVAILALGEVFYIAARARRDKANLETRSAGR 240 IG+DS +GI R+TLG P+L DGI +V V V + A+GE Y + + ++N Sbjct: 181 LIGLDSTSGIARYTLGVPELVDGIEVVLVAVGLFAVGEALY--SLLYQGESNEGRHRLTS 238 Query: 241 PWLTGTEFKEAAPAWARGTIIGLPFGVIPVGGSEVPTFLAYSTERALDKRRKDPQFG-DK 299 W+T ++K + PAW RGT+IG PFG IP GG+E+PTFL+YS ER L K K+ + Sbjct: 239 LWMTRADWKRSVPAWLRGTLIGFPFGSIPAGGAEIPTFLSYSAERKLSKYPKEFSANKGE 298 Query: 300 GAIRGLAAPEAAGNATTGMAMGALLALGLPVSATAAIMLAAFRQYGIQPGPLLFDRNPEL 359 GAI G+A PEAA NA+ ++ LL LG+P SATAAI+LAAF+ Y +QPGP+LF+ + +L Sbjct: 299 GAIEGVAGPEAANNASATGSLVPLLTLGIPTSATAAILLAAFQNYNLQPGPMLFETSADL 358 Query: 360 VWALLASFFIAMIVLLFINLPFAQLWAKLLLIPNHYLYSGIALFCGLGIYATSGAVFDLL 419 VW L+AS +I ++LL +NLP LW KLL IP YL +GI +F +G+Y + FDL+ Sbjct: 359 VWTLVASLYIGNVILLVLNLPLVGLWVKLLQIPRPYLNAGILVFATIGVYGMRHSSFDLI 418 Query: 420 MLLGIGVVALIMRRYGYPLAPLMIGMVLGPLAETSLRDALLSSVGDFSILVSSPITWSLY 479 ++L IG ++MRR+ +P+AP+++GM+LGP+AE LR+AL S GD+++ V+ PI+ Sbjct: 419 LMLAIGWGGVLMRRFDFPVAPVIVGMLLGPMAEKQLRNALSISQGDWTVFVTQPISAFFL 478 Query: 480 AVLAIFIAVSVITAIRGRRKH 500 A+ + + V + RG + H Sbjct: 479 ALTLLVLMVPYVLHKRGIKLH 499 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: 748 Number of extensions: 32 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: 510 Length of database: 502 Length adjustment: 34 Effective length of query: 476 Effective length of database: 468 Effective search space: 222768 Effective search space used: 222768 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