Align The pmf-dependent citrate uptake system, Cit1 (characterized)
to candidate 14895 b0770 predicted transporter (NCBI)
Query= TCDB::Q6D017 (484 letters) >FitnessBrowser__Keio:14895 Length = 477 Score = 297 bits (761), Expect = 5e-85 Identities = 169/471 (35%), Positives = 264/471 (56%), Gaps = 11/471 (2%) Query: 14 MIVILVIAAFFWQMEPPAGLNPAAWHSAVIFVATIVCIVANVLPIGAIGIISITLFALTY 73 +I+IL I M PAGL+ AW I++A IV +V P + +I++ A + Sbjct: 9 LILILAIPCIIGFMPAPAGLSELAWVLFGIYLAAIVGLVIKPFPEPVVLLIAV---AASM 65 Query: 74 AAGDKTASGAIQTA--LSDLNSSLIWLIVVAFMIARGFIKTGLGRRIALQMIRLLGKRTL 131 + GA +T LS +S WL+ AF ++ F+ TGLG+RIA +I +G TL Sbjct: 66 VVVGNLSDGAFKTTAVLSGYSSGTTWLVFSAFTLSAAFVTTGLGKRIAYLLIGKIGNTTL 125 Query: 132 GLAYGLAFADLVLSPAMPSNTARCGGIIYPIADSLSRSFDSKPEDASRSKIGTFLITCIG 191 GL Y F DLVL+PA PSNTAR GGI+ PI +S++ + S+PE + R ++G +L+ I Sbjct: 126 GLGYVTVFLDLVLAPATPSNTARAGGIVLPIINSVAVALGSEPEKSPR-RVGHYLMMSIY 184 Query: 192 NVNDVTAAMFMTAYTGNLLAVKLAAN-AGVTITWGSWFLAALVPCLISLAIVPLLVYWLT 250 V T+ MF TA GN+LA+K+ + + I+WG W LAA +P +I L + PL++Y + Sbjct: 185 MVTKTTSYMFFTAMAGNILALKMINDILHLQISWGGWALAAGLPGIIMLLVTPLVIYTMY 244 Query: 251 KPEIRHTPDAPKLAVAELAKMGSISRGEWLMAFTVILLLVLWIFGDRLGVDATTASFVGL 310 PEI+ D +A A LA++G + E ++ +L L+ WIF LGVD +T + V + Sbjct: 245 PPEIKKV-DNKTIAKAGLAELGPMKIREKMLLGVFVLALLGWIFSKSLGVDESTVAIVVM 303 Query: 311 SFLLLTGVLSWEDVKNEKGAWDTLIWFAALLMMANQLKKLGFTNWFGDLIGSNIGHLMQG 370 + +LL G+++WEDV KG W+TLIW+ ++ +++ L K+ F W ++ +N+ G Sbjct: 304 ATMLLLGIVTWEDVVKNKGGWNTLIWYGGIIGLSSLLSKVKFFEWLAEVFKNNLAFDGHG 363 Query: 371 TSWVLVLLLLNAAYFYTHYFFASGNAQIAALFAVFLGVGINLNIPAVPMAFMLAFTSSLY 430 V++ L+ YFFASG+A I A+ VF + P + A L F++S Sbjct: 364 NVAFFVIIFLS---IIVRYFFASGSAYIVAMLPVFAMLANVSGAPLMLTALALLFSNSYG 420 Query: 431 CSLTQYTHARGPILFGAGYVPTAVWWRTGFVVSLVNQAIFMGAGLLWWKAI 481 +T Y A GP++FG GY WW G V++++ + + G+ WW + Sbjct: 421 GMVTHYGGAAGPVIFGVGYNDIKSWWLVGAVLTILTFLVHITLGVWWWNML 471 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: 807 Number of extensions: 48 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: 477 Length adjustment: 34 Effective length of query: 450 Effective length of database: 443 Effective search space: 199350 Effective search space used: 199350 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