Align aerobic C4-dicarboxylate transport protein (characterized)
to candidate PfGW456L13_1449 probable dicarboxylate transporter
Query= CharProtDB::CH_014038 (428 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1449 Length = 420 Score = 399 bits (1024), Expect = e-115 Identities = 201/400 (50%), Positives = 283/400 (70%), Gaps = 1/400 (0%) Query: 19 IGILLGHFYPEIGEQMKPLGDGFVKLIKMIIAPVIFCTVVTGIAGMESMKAVGRTGAVAL 78 +GI+ G PE Q+KPLGDGF+KLIKM+I ++FC VV+GI+G +K VGR G ++ Sbjct: 2 LGIVCGLTLPEYSAQLKPLGDGFIKLIKMLIGLIVFCVVVSGISGAGDLKKVGRIGLKSV 61 Query: 79 LYFEIVSTIALIIGLIIVNVVQPGAGMNVDPATLDAKAVAVYADQAKDQGIVA-FIMDVI 137 +YFE+++TIAL+IGL+ G+G N+ L A + A + + F+MD+I Sbjct: 62 IYFEVLTTIALVIGLVFAFSTGIGSGANIHLEQLSAADMGDIAQRGQHMHTTTQFLMDLI 121 Query: 138 PASVIGAFASGNILQVLLFAVLFGFALHRLGSKGQLIFNVIESFSQVIFGIINMIMRLAP 197 P SVIGAFA NILQVLLF+VLFG AL+ +G I +I S VIF I+ MI+RLAP Sbjct: 122 PTSVIGAFADNNILQVLLFSVLFGSALNLVGEAASGISRLINELSHVIFRIMGMIVRLAP 181 Query: 198 IGAFGAMAFTIGKYGVGTLVQLGQLIICFYITCILFVVLVLGSIAKATGFSIFKFIRYIR 257 IG FGA+AFT KYG+ +L LG L+ FY+TC+ FV L+LG + + +G ++ ++Y+R Sbjct: 182 IGVFGAIAFTTSKYGLDSLQHLGSLVGLFYLTCVAFVALILGLVMRLSGLKMWPLLKYLR 241 Query: 258 EELLIVLGTSSSESALPRMLDKMEKLGCRKSVVGLVIPTGYSFNLDGTSIYLTMAAVFIA 317 EELLIV+GT+SS++ LP+++ K+E LG S VGLVIPTGYSFNLDG SIYLT+A VFIA Sbjct: 242 EELLIVMGTASSDAVLPQIMRKLEHLGIGSSTVGLVIPTGYSFNLDGFSIYLTLAIVFIA 301 Query: 318 QATNSQMDIVHQITLLIVLLLSSKGAAGVTGSGFIVLAATLSAVGHLPVAGLALILGIDR 377 AT + + + +T+L+V L++SKGA G+ GS ++LAATL+A+ +PV GL L+L +D Sbjct: 302 NATGTPLAMTDLLTILLVSLITSKGAHGIPGSALVILAATLTAIPAIPVVGLVLVLAVDW 361 Query: 378 FMSEARALTNLVGNGVATIVVAKWVKELDHKKLDDVLNNR 417 FM RALTNL+GN VAT+ +A+W K++D ++ + VL+ + Sbjct: 362 FMGIGRALTNLIGNCVATVAIARWEKDIDIQRANKVLSGQ 401 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: 546 Number of extensions: 37 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 428 Length of database: 420 Length adjustment: 32 Effective length of query: 396 Effective length of database: 388 Effective search space: 153648 Effective search space used: 153648 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