Align C4-dicarboxylate transport protein 2 (characterized)
to candidate RR42_RS01695 RR42_RS01695 C4-dicarboxylate transporter
Query= SwissProt::Q9I4F5 (436 letters) >FitnessBrowser__Cup4G11:RR42_RS01695 Length = 433 Score = 538 bits (1385), Expect = e-157 Identities = 271/433 (62%), Positives = 341/433 (78%) Query: 1 MTKQPFYKSLYVQVLVAIAIGIALGHWYPETAVAMKPFGDGFVKLIKMAIAPIIFCTVVT 60 M ++PFYK LYVQVL AIA+GI LGH++P T VAMKP GDGF+KLIKM I PIIFCTVV+ Sbjct: 1 MMRKPFYKILYVQVLFAIAVGIVLGHFWPATGVAMKPLGDGFIKLIKMIIGPIIFCTVVS 60 Query: 61 GIAGMQSMKSVGKTGGMALLYFEVVSTVALIIGLVVVNVVQPGAGMHVDPNTLDTSKIAA 120 GIAGM+ MK VG+ GG ALLYFEV+ST AL+IGL+ ++++PG G ++DP TLDT I+ Sbjct: 61 GIAGMRDMKKVGRVGGKALLYFEVISTFALLIGLLSAHLLKPGVGFNIDPATLDTKAISQ 120 Query: 121 YAAAGEKQSTVDFLMNVIPGTVVGAFANGDILQVLFFSVLFGYALHRLGSYGKPVFEFIE 180 Y QSTV+F M++IP T+V AFANGDILQ+L S+ FG AL +G K VF+F+E Sbjct: 121 YVTQAHGQSTVEFFMHIIPDTMVSAFANGDILQILLISLFFGSALAAMGDRSKIVFDFVE 180 Query: 181 RVSHVMFNIINVIMKVAPIGAFGAMAFTIGAYGVGSLVQLGQLMLCFYITCILFVLIVLG 240 +VS V F+I++VI KVAP+GAFGAMAFTIG YG+GSLV L +L+ FY T I+FV++VLG Sbjct: 181 QVSKVFFHIVHVITKVAPLGAFGAMAFTIGKYGLGSLVPLLKLIGTFYFTAIVFVVVVLG 240 Query: 241 GIARAHGFSILRFIRYIREELLIVLGTSSSESALPRMIDKMEKLGCNKSVVGLVIPTGYS 300 +AR GF+I RFI YI+EELLIVLGTSSSE+ALP +++K+E LGC+KSVVGLV+PTGYS Sbjct: 241 TVARLTGFNIFRFISYIKEELLIVLGTSSSEAALPHLMEKLENLGCSKSVVGLVVPTGYS 300 Query: 301 FNLDGTSIYLTMAAVFIAQATDTPMDITHQITLLLVLLIASKGAAGVTGSGFIVLAATLS 360 FNLDGT+IY+TMA +FIAQAT + + Q+T+L V +I SKGA+GVTGSGFI LAATL+ Sbjct: 301 FNLDGTNIYMTMAVLFIAQATGIELTLLQQLTVLGVAMITSKGASGVTGSGFITLAATLA 360 Query: 361 AVGHLPVAGLALILGIDRFMSEARALTNLVGNGVATVVVSKWCKQLDEGTLQRELAGEGN 420 V +PVAG+ LILGIDRFMSE RALTN++GNGVATVV+S W +LD L R L G+ Sbjct: 361 VVPDIPVAGMVLILGIDRFMSECRALTNIIGNGVATVVMSAWEHELDRVQLDRMLRRGGD 420 Query: 421 ASSPASDIPVGGR 433 ++ ++ G R Sbjct: 421 ETAELAEAGPGVR 433 Lambda K H 0.325 0.140 0.406 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: 641 Number of extensions: 29 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: 436 Length of database: 433 Length adjustment: 32 Effective length of query: 404 Effective length of database: 401 Effective search space: 162004 Effective search space used: 162004 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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