Align The pmf-dependent citrate uptake system, Cit1 (characterized)
to candidate HSERO_RS04820 HSERO_RS04820 C4-dicarboxylate ABC transporter
Query= TCDB::Q6D017 (484 letters) >FitnessBrowser__HerbieS:HSERO_RS04820 Length = 501 Score = 386 bits (992), Expect = e-112 Identities = 198/463 (42%), Positives = 283/463 (61%), Gaps = 14/463 (3%) Query: 30 PAGLNPAAWHSAVIFVATIVCIVANVLPIGAIGIISITLFALTYAAGDKTASGAIQTALS 89 P GL P AW IF+ TIV I+ V+PIG + +++I + +L+ ++ GAI AL+ Sbjct: 39 PTGLEPKAWALVAIFLTTIVAIILKVMPIGVMAMMAIVIVSLSQVTST-SSKGAITDALA 97 Query: 90 DLNSSLIWLIVVAFMIARGFIKTGLGRRIALQMIRLLGKRTLGLAYGLAFADLVLSPAMP 149 ++ LIWLIVVA +I+RG KTGLGRR+ L I LLGKRT+G+ YGLA +LVL+P P Sbjct: 98 SFSNPLIWLIVVAILISRGLKKTGLGRRVGLMFIALLGKRTIGIGYGLAICELVLAPFTP 157 Query: 150 SNTARCGGIIYPIADSLSRSFDSKPEDASRSKIGTFLITCIGNVNDVTAAMFMTAYTGNL 209 SNTAR GGI++PI S++ +FDS P +++K+G++L + N +T+AMF+TA N Sbjct: 158 SNTARGGGIVHPIMKSIANAFDSDPAKGTQNKVGSYLALVNYHANPITSAMFLTATAPNP 217 Query: 210 LAVKLAANA---GVTITWGSWFLAALVPCLISLAIVPLLVYWLTKPEIRHTPDAPKLAVA 266 L V A A + +TW +W L L+P L+ L I+P+++Y L+ PE++ TP+A A + Sbjct: 218 LVVNYVAKATGHALQLTWTTWALCMLLPGLVCLLIMPMVIYLLSPPELKSTPNAVDYARS 277 Query: 267 ELAKMGSISRGEWLMAFTVILLLVLW------IFGDRLGVDATTASFVGLSFLLLTGVLS 320 EL KMG + E +M T LLL+LW + G +D T +FVGL L++TG + Sbjct: 278 ELDKMGKLGASEKVMLGTFALLLLLWANVPAMLLGAAFTLDPTVVAFVGLFVLIITGTID 337 Query: 321 WEDVKNEKGAWDTLIWFAALLMMANQLKKLGFTNWFGDLIGSNIGHLMQGTSWVLVLLLL 380 W+DV +EK AWDTL+WF AL+M+A QL K G WF + G + G W+ V +L Sbjct: 338 WDDVLSEKSAWDTLVWFGALVMLAEQLNKTGVVAWFSE--GMKAAIVASGMGWIAVAAVL 395 Query: 381 NAAYFYTHYFFASGNAQIAALFAVFLGVGINLNIPAVPMAFMLAFT--SSLYCSLTQYTH 438 + +HYFFAS A I+A+ FL VG L P + FML T S + +LT Y Sbjct: 396 LLVFVLSHYFFASTTAHISAMMLAFLTVGAQLLPPQYVVPFMLMMTAGSGVMMTLTHYAT 455 Query: 439 ARGPILFGAGYVPTAVWWRTGFVVSLVNQAIFMGAGLLWWKAI 481 PI+FG+GYV WW GFV+++V +F G++WWK + Sbjct: 456 GTSPIIFGSGYVSMGKWWGVGFVMAVVELLVFATVGMVWWKGL 498 Lambda K H 0.327 0.139 0.440 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: 821 Number of extensions: 57 Number of successful extensions: 6 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: 484 Length of database: 501 Length adjustment: 34 Effective length of query: 450 Effective length of database: 467 Effective search space: 210150 Effective search space used: 210150 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: 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