Align Citrate uptake transporter, membrane subunit, component of Pmf-dependent citrate uptake porter, TctABC (characterized)
to candidate SM_b20726 SM_b20726 hypothetical protein
Query= TCDB::S5Y5N9 (510 letters) >FitnessBrowser__Smeli:SM_b20726 Length = 505 Score = 484 bits (1245), Expect = e-141 Identities = 242/497 (48%), Positives = 337/497 (67%), Gaps = 4/497 (0%) Query: 1 MDILSLLMEGFAGALTPMNLLWVIVGCLLGTAVGVMPGLGSSMAVALLLPMTFALDPTAA 60 M L++G A PMNLL+ ++G LGTAVGV+PG+G ++ VALLLP+T+ LDP + Sbjct: 1 MGTFDFLLQGLLVAAQPMNLLYALIGVTLGTAVGVLPGIGPALTVALLLPVTYQLDPAGS 60 Query: 61 FIMFSGVYFGGLFGDSTMAILMNTPGQASAIASTFEGHRMALNGRAPQALATAAIGAFIG 120 IMF+G+Y+GG++G ST +IL+NTPG++++I + EG++MA GR ALATAAIG+F+ Sbjct: 61 LIMFAGIYYGGMYGGSTTSILLNTPGESASIVTALEGNKMARAGRGGPALATAAIGSFVA 120 Query: 121 GIVSSFIVVFLAPTLAELSTAFGPAEYFALALFAFVATSSVVSDSVFKGLASLIFGLGIA 180 G++++ + F+AP + +L+ FGP EYFAL + AFV SS DS +GL SL GL +A Sbjct: 121 GLIATLGLAFIAPYIVKLALVFGPREYFALMVLAFVTVSSAFGDSTLRGLTSLFIGLTLA 180 Query: 181 TIGIDSVTGIERFTLGAPQLFDGISLVTVTVAILALGEVFYIAARARRDKANLETRSAGR 240 IGID +TG R + G P L DGI + T+ VA+ A+GE +IAA+ R +E G Sbjct: 181 CIGIDQLTGQARLSFGVPDLLDGIEVTTLAVAMFAIGETLFIAAQGDRGPDKVEA-VRGS 239 Query: 241 PWLTGTEFKEAAPAWARGTIIGLPFGVIPVGGSEVPTFLAYSTERALDKRRKDPQFGDKG 300 W++ T++ + W RGT IG P G +P GG+E+ TFL+Y+ E+ L K + +FG+ G Sbjct: 240 VWMSATDWARSWKPWLRGTFIGFPIGAMPAGGAEIGTFLSYAAEKRLTKHPE--EFGN-G 296 Query: 301 AIRGLAAPEAAGNATTGMAMGALLALGLPVSATAAIMLAAFRQYGIQPGPLLFDRNPELV 360 AI G+A PEAA NA+ + LL LGLP +ATAAIMLA F+QYG+QPGPLLF NP+LV Sbjct: 297 AIEGVAGPEAANNASAAGTLVPLLTLGLPTTATAAIMLAGFQQYGLQPGPLLFATNPQLV 356 Query: 361 WALLASFFIAMIVLLFINLPFAQLWAKLLLIPNHYLYSGIALFCGLGIYATSGAVFDLLM 420 W L+AS IA +LL +NLP LW KLL IP +LY+GI LF LG + +VF+L M Sbjct: 357 WGLIASLLIANFMLLVLNLPLIGLWVKLLTIPKPWLYAGILLFATLGTIGANPSVFELGM 416 Query: 421 LLGIGVVALIMRRYGYPLAPLMIGMVLGPLAETSLRDALLSSVGDFSILVSSPITWSLYA 480 LL G++ +MR +GYP+AP+++G++LGPLAE LR AL S GD ++L +SPI L Sbjct: 417 LLAFGLLGYVMRVFGYPIAPVVVGLILGPLAEQQLRRALSISQGDITVLFTSPIAAVLLV 476 Query: 481 VLAIFIAVSVITAIRGR 497 + A+ + V +I RGR Sbjct: 477 IAALALVVPLILRARGR 493 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: 790 Number of extensions: 44 Number of successful extensions: 4 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: 505 Length adjustment: 34 Effective length of query: 476 Effective length of database: 471 Effective search space: 224196 Effective search space used: 224196 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