Align Citrate uptake transporter, substrate binding protein, component of Pmf-dependent citrate uptake porter, TctABC (characterized)
to candidate AZOBR_RS31445 AZOBR_RS31445 C4-dicarboxylate ABC transporter substrate-binding protein
Query= TCDB::S5XTE7 (334 letters) >FitnessBrowser__azobra:AZOBR_RS31445 Length = 323 Score = 224 bits (570), Expect = 3e-63 Identities = 126/316 (39%), Positives = 183/316 (57%), Gaps = 7/316 (2%) Query: 22 GTAAVVITAIAAFFSIQSASGGEDIRSNMTLIAPAAAGGGWDTFQREQQQSMRVNKIVNN 81 G A + A AA F+ A +I+ N+ +IAPA AGGG+D R QQ ++ +K+ ++ Sbjct: 9 GMLAAAVLAAAALFA---APASAEIK-NLEIIAPANAGGGYDQHARAMQQVLQEHKLASS 64 Query: 82 IQVVNIPGAGGTIALGKLSTMTAPNT-LMVGGTGHIAAQIQFDTPAKIQDVTPIARVVEE 140 +QVVNIPGAGGTI L + T N LM+ G G I A + +P + VTP+AR+ E Sbjct: 65 VQVVNIPGAGGTIGLSQFVTAKKRNPGLMISGLGMIGAILINKSPVSLDQVTPLARLTGE 124 Query: 141 FDIITVPADSPYNTLEELIEGWKADPAGVSWTGG--GSFDQLVMTEIALSAGIDPKQTTF 198 + I V ADSP TL++L++ +KADP VSW G GS D ++ + + G D + + Sbjct: 125 YQPIVVAADSPLKTLDDLVKKFKADPGSVSWGGFAVGSPDHILYGLLVKAIGGDVSKMNY 184 Query: 199 IPSDGGGEAIQALLNGTAKASTGGFADMYPQVEAGRLKVLGIAAEERLPGSDIPTLVEQG 258 I + GGE + ++L G +TGG+ +M Q++AG+L+ L I+A +RLPG D+PT EQG Sbjct: 185 IAAGAGGEMMASVLGGHITVATGGYNEMASQLQAGKLRALAISAPQRLPGIDVPTFKEQG 244 Query: 259 YDVTLTNWRAMFAPPGLSDDQIAELRAIVAESVETAEWQSAVERNYWMNASLEGEELDQF 318 DV L NWRA+ AP L + L V V T EW+ E W++ L + F Sbjct: 245 VDVELVNWRAVMAPGNLKASEKQVLDDAVGAMVRTDEWKRIAEERGWIDLYLPPDRFAAF 304 Query: 319 VEDEIDRIDQLFKEMG 334 V+DE RI+ + E+G Sbjct: 305 VKDERTRIEGVLMELG 320 Lambda K H 0.314 0.131 0.375 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: 327 Number of extensions: 16 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: 334 Length of database: 323 Length adjustment: 28 Effective length of query: 306 Effective length of database: 295 Effective search space: 90270 Effective search space used: 90270 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 49 (23.5 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