Align Citrate:Na+ symporter, CitS (characterized)
to candidate BWI76_RS04430 BWI76_RS04430 citrate carrier protein
Query= TCDB::P31602 (446 letters) >FitnessBrowser__Koxy:BWI76_RS04430 Length = 446 Score = 829 bits (2141), Expect = 0.0 Identities = 421/446 (94%), Positives = 440/446 (98%) Query: 1 MTNMSQPPATEKKGVSDLLGFKIFGMPLPLYAFALITLLLSHFYNALPTDIVGGFAIMFI 60 MTNMSQ P+ EKKGVSD+LGFKIFGMPLPLYAFALITLLLSHFYNALPTDIVGGFAIMFI Sbjct: 1 MTNMSQAPSAEKKGVSDILGFKIFGMPLPLYAFALITLLLSHFYNALPTDIVGGFAIMFI 60 Query: 61 IGAIFGEIGKRLPIFNKYIGGAPVMIFLVAAYFVYAGIFTQKEIDAISNVMDKSNFLNLF 120 IGA+FGEIGKRLPIFNKYIGGAPVMIFLVAAYFVYAGIFTQKEI+AI+NVMDKSNFLNLF Sbjct: 61 IGAVFGEIGKRLPIFNKYIGGAPVMIFLVAAYFVYAGIFTQKEIEAITNVMDKSNFLNLF 120 Query: 121 IAVLITGAILSVNRRLLLKSLLGYIPTILMGIVGASIFGIAIGLVFGIPVDRIMMLYVLP 180 IAVLITGAILSVNR+LLLKSLLGYIPTILMGI+GASIFGI IGL FGI VDRIMMLYVLP Sbjct: 121 IAVLITGAILSVNRKLLLKSLLGYIPTILMGILGASIFGILIGLCFGISVDRIMMLYVLP 180 Query: 181 IMGGGNGAGAVPLSEIYHSVTGRSREEYYSTAIAILTIANIFAIVFAAVLDIIGKKHTWL 240 IMGGGNGAGAVPLSEIYHSVTGRSREEYYSTAIAILTIANIFAIVFAA+LDIIGKKHTWL Sbjct: 181 IMGGGNGAGAVPLSEIYHSVTGRSREEYYSTAIAILTIANIFAIVFAALLDIIGKKHTWL 240 Query: 241 SGEGELVRKASFKVEEDEKTGQITHRETAVGLVLSTTCFLLAYVVAKKILPSIGGVAIHY 300 SGEGELVRKASFKVE+DEK GQITHRETAVGLVL+TTCFLLAYV+AKKILPSIGGV+IHY Sbjct: 241 SGEGELVRKASFKVEDDEKAGQITHRETAVGLVLATTCFLLAYVIAKKILPSIGGVSIHY 300 Query: 301 FAWMVLIVAALNASGLCSPEIKAGAKRLSDFFSKQLLWVLMVGVGVCYTDLQEIINAITF 360 FAWMVLIVAALNASGLCSPEIKAGAKRLSDFFSKQLLWVLMVGVGVCYTDLQEII+AITF Sbjct: 301 FAWMVLIVAALNASGLCSPEIKAGAKRLSDFFSKQLLWVLMVGVGVCYTDLQEIIDAITF 360 Query: 361 ANVVIAAIIVIGAVLGAAIGGWLMGFFPIESAITAGLCMANRGGSGDLEVLSACNRMNLI 420 ANVVIAA+IV+GAV+GAA+GGWL+GFFPIESAITAGLCMANRGGSGDLEVLSACNRMNLI Sbjct: 361 ANVVIAAVIVVGAVVGAAVGGWLIGFFPIESAITAGLCMANRGGSGDLEVLSACNRMNLI 420 Query: 421 SYAQISSRLGGGIVLVIASIVFGMMI 446 SYAQISSRLGGGIVLVIASIVFGMM+ Sbjct: 421 SYAQISSRLGGGIVLVIASIVFGMMM 446 Lambda K H 0.327 0.144 0.420 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: 808 Number of extensions: 31 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: 446 Length of database: 446 Length adjustment: 32 Effective length of query: 414 Effective length of database: 414 Effective search space: 171396 Effective search space used: 171396 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 (21.7 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