Align aerobic C4-dicarboxylate transport protein (characterized)
to candidate RR42_RS01695 RR42_RS01695 C4-dicarboxylate transporter
Query= CharProtDB::CH_014038 (428 letters) >FitnessBrowser__Cup4G11:RR42_RS01695 Length = 433 Score = 525 bits (1351), Expect = e-153 Identities = 258/427 (60%), Positives = 342/427 (80%), Gaps = 2/427 (0%) Query: 1 MKTSLFKSLYFQVLTAIAIGILLGHFYPEIGEQMKPLGDGFVKLIKMIIAPVIFCTVVTG 60 M+ +K LY QVL AIA+GI+LGHF+P G MKPLGDGF+KLIKMII P+IFCTVV+G Sbjct: 2 MRKPFYKILYVQVLFAIAVGIVLGHFWPATGVAMKPLGDGFIKLIKMIIGPIIFCTVVSG 61 Query: 61 IAGMESMKAVGRTGAVALLYFEIVSTIALIIGLIIVNVVQPGAGMNVDPATLDAKAVAVY 120 IAGM MK VGR G ALLYFE++ST AL+IGL+ ++++PG G N+DPATLD KA++ Y Sbjct: 62 IAGMRDMKKVGRVGGKALLYFEVISTFALLIGLLSAHLLKPGVGFNIDPATLDTKAISQY 121 Query: 121 ADQAKDQGIVAFIMDVIPASVIGAFASGNILQVLLFAVLFGFALHRLGSKGQLIFNVIES 180 QA Q V F M +IP +++ AFA+G+ILQ+LL ++ FG AL +G + +++F+ +E Sbjct: 122 VTQAHGQSTVEFFMHIIPDTMVSAFANGDILQILLISLFFGSALAAMGDRSKIVFDFVEQ 181 Query: 181 FSQVIFGIINMIMRLAPIGAFGAMAFTIGKYGVGTLVQLGQLIICFYITCILFVVLVLGS 240 S+V F I+++I ++AP+GAFGAMAFTIGKYG+G+LV L +LI FY T I+FVV+VLG+ Sbjct: 182 VSKVFFHIVHVITKVAPLGAFGAMAFTIGKYGLGSLVPLLKLIGTFYFTAIVFVVVVLGT 241 Query: 241 IAKATGFSIFKFIRYIREELLIVLGTSSSESALPRMLDKMEKLGCRKSVVGLVIPTGYSF 300 +A+ TGF+IF+FI YI+EELLIVLGTSSSE+ALP +++K+E LGC KSVVGLV+PTGYSF Sbjct: 242 VARLTGFNIFRFISYIKEELLIVLGTSSSEAALPHLMEKLENLGCSKSVVGLVVPTGYSF 301 Query: 301 NLDGTSIYLTMAAVFIAQATNSQMDIVHQITLLIVLLLSSKGAAGVTGSGFIVLAATLSA 360 NLDGT+IY+TMA +FIAQAT ++ ++ Q+T+L V +++SKGA+GVTGSGFI LAATL+ Sbjct: 302 NLDGTNIYMTMAVLFIAQATGIELTLLQQLTVLGVAMITSKGASGVTGSGFITLAATLAV 361 Query: 361 VGHLPVAGLALILGIDRFMSEARALTNLVGNGVATIVVAKWVKELDHKKLDDVLNNRAPD 420 V +PVAG+ LILGIDRFMSE RALTN++GNGVAT+V++ W ELD +LD +L R Sbjct: 362 VPDIPVAGMVLILGIDRFMSECRALTNIIGNGVATVVMSAWEHELDRVQLDRML--RRGG 419 Query: 421 GKTHELS 427 +T EL+ Sbjct: 420 DETAELA 426 Lambda K H 0.327 0.142 0.401 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: 601 Number of extensions: 24 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: 428 Length of database: 433 Length adjustment: 32 Effective length of query: 396 Effective length of database: 401 Effective search space: 158796 Effective search space used: 158796 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