Align aerobic C4-dicarboxylate transport protein (characterized)
to candidate GFF2942 PS417_15055 C4-dicarboxylate ABC transporter
Query= CharProtDB::CH_014038 (428 letters) >FitnessBrowser__WCS417:GFF2942 Length = 436 Score = 405 bits (1042), Expect = e-117 Identities = 202/412 (49%), Positives = 291/412 (70%), Gaps = 1/412 (0%) Query: 7 KSLYFQVLTAIAIGILLGHFYPEIGEQMKPLGDGFVKLIKMIIAPVIFCTVVTGIAGMES 66 +S++ QV+ + +GI+ G PE Q+KPLGDGF+KLIKM+I ++FC VV+GI+G Sbjct: 7 RSIFLQVVIGLMLGIICGLTLPEFSSQLKPLGDGFIKLIKMLIGLIVFCVVVSGISGAGD 66 Query: 67 MKAVGRTGAVALLYFEIVSTIALIIGLIIVNVVQPGAGMNVDPATLDAKAVAVYADQAKD 126 +K VGR G +++YFEI++T+AL+IGL++ G G N+ L + + AD+ + Sbjct: 67 LKKVGRIGLKSVIYFEILTTVALVIGLVMAFSTGIGTGANIHLEQLSSAGLNELADKGQH 126 Query: 127 -QGIVAFIMDVIPASVIGAFASGNILQVLLFAVLFGFALHRLGSKGQLIFNVIESFSQVI 185 +G F+MD+IP SVIGAFA N+LQVLLF+VLFG AL+ +G I +I S +I Sbjct: 127 IRGTSQFLMDLIPNSVIGAFADNNVLQVLLFSVLFGSALNLVGEAASGISRLINELSHII 186 Query: 186 FGIINMIMRLAPIGAFGAMAFTIGKYGVGTLVQLGQLIICFYITCILFVVLVLGSIAKAT 245 F I+ MI+RLAPIG FGA+AFT YG+ +L LG L+ FY+TC FV L+LG + + + Sbjct: 187 FRIMGMIVRLAPIGVFGAIAFTTSTYGLDSLQHLGSLVGLFYLTCFAFVGLILGLVMRLS 246 Query: 246 GFSIFKFIRYIREELLIVLGTSSSESALPRMLDKMEKLGCRKSVVGLVIPTGYSFNLDGT 305 G + ++Y+REELLIV+GT+SS++ LP+++ K+E LG S VGLVIPTGYSFNLDG Sbjct: 247 GLRMLPLLKYLREELLIVMGTASSDAVLPQIMRKLEHLGIGSSTVGLVIPTGYSFNLDGF 306 Query: 306 SIYLTMAAVFIAQATNSQMDIVHQITLLIVLLLSSKGAAGVTGSGFIVLAATLSAVGHLP 365 SIYLT+A VFIA AT + + + +T+L+V L++SKGA G+ GS ++LAATL+A+ +P Sbjct: 307 SIYLTLAIVFIANATGTPLSMTDLLTILLVSLITSKGAHGIPGSALVILAATLTAIPAIP 366 Query: 366 VAGLALILGIDRFMSEARALTNLVGNGVATIVVAKWVKELDHKKLDDVLNNR 417 V GL L+L +D FM RALTNL+GN VAT+ +A+W K++D ++ + VL+ + Sbjct: 367 VVGLVLVLAVDWFMGIGRALTNLIGNCVATVAIARWEKDIDIQRANKVLDGQ 418 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: 579 Number of extensions: 41 Number of successful extensions: 2 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: 436 Length adjustment: 32 Effective length of query: 396 Effective length of database: 404 Effective search space: 159984 Effective search space used: 159984 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