Align Citrate:H+ symporter (characterized)
to candidate GFF1423 PS417_07230 citrate-proton symporter
Query= TCDB::P16482 (444 letters) >FitnessBrowser__WCS417:GFF1423 Length = 435 Score = 651 bits (1679), Expect = 0.0 Identities = 319/424 (75%), Positives = 365/424 (86%), Gaps = 2/424 (0%) Query: 13 TAPVRMMATAGGARIGAILRVTSGNFLEQFDFFLFGFYATYIAHTFFPASSEFASLMMTF 72 T+P R + +++GA+ RVTSGNFLEQFDFFLFGFYATYIA FFPA++EFASLMMTF Sbjct: 2 TSPTR--PDSARSKVGAVFRVTSGNFLEQFDFFLFGFYATYIAAAFFPAANEFASLMMTF 59 Query: 73 AVFGAGFLMRPIGAIVLGAYIDKVGRRKGLIVTLSIMATGTFLIVLIPSYQTIGLWAPLL 132 AVFGAGFLMRP+GAI+LGAYID VGRRKGLIVTLSIMA+GT LIVL+PSY TIGLWAPLL Sbjct: 60 AVFGAGFLMRPLGAIILGAYIDDVGRRKGLIVTLSIMASGTLLIVLVPSYHTIGLWAPLL 119 Query: 133 VLIGRLLQGFSAGAELGGVSVYLAEIATPGRKGFYTSWQSGSQQVAIMVAAAMGFALNAV 192 VL+GRLLQGFSAGAELGGVSVYL+E+ATPGRKGFYTSWQSGSQQ++I+VAAA+G+ LN Sbjct: 120 VLLGRLLQGFSAGAELGGVSVYLSEMATPGRKGFYTSWQSGSQQISIVVAAALGYGLNVW 179 Query: 193 LEPSAISDWGWRIPFLFGVLIVPFIFILRRKLEETQEFTARRHHLAMRQVFATLLANWQV 252 +EP+ ++DWGWRIPF G +I+PFIFILRR L+ET+EF R+H MR+V ATL+ NW V Sbjct: 180 MEPAVVADWGWRIPFAIGCVIIPFIFILRRSLQETEEFANRKHRPTMREVLATLVKNWTV 239 Query: 253 VIAGMMMVAMTTTAFYLITVYAPTFGKKVLMLSASDSLLVTLLVAISNFFWLPVGGALSD 312 VI GM+MVAMTTTAFYLITVYAPTFGK VL LS SD+LLVTLLVA+SNF WLP+GG LSD Sbjct: 240 VIGGMLMVAMTTTAFYLITVYAPTFGKTVLQLSTSDALLVTLLVAVSNFIWLPIGGTLSD 299 Query: 313 RFGRRSVLIAMTLLALATAWPALTMLANAPSFLMMLSVLLWLSFIYGMYNGAMIPALTEI 372 RFGR+ VLIAMT+L + TA+PAL+ + NAPSF ML LLW SF+YG+YNGAMIPALTEI Sbjct: 300 RFGRKPVLIAMTVLTVLTAYPALSYVVNAPSFAHMLETLLWFSFLYGLYNGAMIPALTEI 359 Query: 373 MPAEVRVAGFSLAYSLATAVFGGFTPVISTALIEYTGDKASPGYWMSFAAICGLLATCYL 432 MP EVRVAGFSLAYSLATA+FGGFTP IST I T DKASP YWM FAA C L +T L Sbjct: 360 MPVEVRVAGFSLAYSLATAIFGGFTPAISTWFIHITEDKASPAYWMMFAAACALCSTLAL 419 Query: 433 YRRS 436 YRR+ Sbjct: 420 YRRA 423 Lambda K H 0.329 0.139 0.421 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: 711 Number of extensions: 18 Number of successful extensions: 1 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: 444 Length of database: 435 Length adjustment: 32 Effective length of query: 412 Effective length of database: 403 Effective search space: 166036 Effective search space used: 166036 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 (21.9 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