Align Tricarboxylic transport TctA (characterized, see rationale)
to candidate HSERO_RS16690 HSERO_RS16690 C4-dicarboxylate ABC transporter permease
Query= uniprot:E4PJQ9 (508 letters) >FitnessBrowser__HerbieS:HSERO_RS16690 Length = 498 Score = 287 bits (734), Expect = 7e-82 Identities = 164/488 (33%), Positives = 266/488 (54%), Gaps = 5/488 (1%) Query: 11 FAVALTPYNLMFALFGAFVGTLIGCLPGLGPANGVAILIPLAFTLGLPPETAMILLTAVY 70 F + PY L L + G +G +PGL VA+L+P+ F + PP A+ + + Sbjct: 9 FGMVFDPYVLAVILGSSIFGLFMGAVPGLSATMAVALLVPVTFFM--PPVPAIAAMVSAT 66 Query: 71 AGAMYGGRISSILLNIPGDEPAMMTCLDGYPMAQKGRAADALAVSAIASFAGGLIGTIGL 130 A A++ G I LL IPG + + Y M KG+ AL S + S GGL GT L Sbjct: 67 AMAIFSGDIPGCLLRIPGTPSSAAYTDEAYAMTMKGQGEIALGASLVFSVIGGLFGTFVL 126 Query: 131 IMLAPVLAKFALTFGPAEYFALFLLAFATLGGITGKNPVKTVVAATLGIMISTVGIDIST 190 I+ AP LA+ AL F EYF L LL I NP+K V+ LG+ I+++G+ Sbjct: 127 ILAAPALAELALKFSSFEYFWLVLLGLTCAIFIASDNPLKGFVSLFLGMFIASIGMGNPA 186 Query: 191 GTQRYTFGVLELYEGIDFILAIVGLFAISELLFFVESR-MGRGRDKMNVGKLTLTMKELV 249 G R+TF +L G+ + +VG+FA+SE+L F SR + VG + M L+ Sbjct: 187 GAPRFTFDQPDLLGGVSLVPLMVGMFAMSEVLRFAVSRDFSMKVAESRVGNVFKGMWGLM 246 Query: 250 MTIPTQ-LRGGVLGFISGVLPGAGASLGSFISYTLEKQVVGKKGKFGEGDIRGVVAPEAG 308 + P LRG VLG + G LPGAGA + +++SY + K++ + KFG G G+V A Sbjct: 247 IKYPKSVLRGSVLGTLVGALPGAGADIAAWMSYAMSKKLSKEPEKFGTGHPEGIVESGAA 306 Query: 309 NNGASSGALVPMLTLGVPGSGTTAVLLAMLISLNITPGPLMFTQNADIVWGVIAALLIGN 368 NN A +GA +P L G+PG TA+++ +L N+ PGP++F +N ++ + ++ N Sbjct: 307 NNSALAGAWIPALVFGIPGDSITAIVIGVLYMKNLNPGPMIFVENPVSMYAIFIVFILAN 366 Query: 369 VLLLVLNIPLVGFFVKLLSVPPMYLLPIVTMVAFVGIYSISHSTFDLYFMVAFGVAGYFL 428 +L+L L + ++LS+P L+P++ + VG Y+ ++S D+ M+ FG+ Y + Sbjct: 367 LLMLPLGFWCIKMAKRILSIPRGILMPLILLFCIVGSYATNNSVTDVGIMLVFGLLAYVM 426 Query: 429 RKLEIPLVPIILGLLLGPEMEKNLGHALVLSDGEWSVLWASPLAMGLWIVAGLGLILPYL 488 + P+ P +LG++LG +E++ +++ +DG++ + P+A L ++ L +LP L Sbjct: 427 EENGFPVAPAVLGVVLGGMLEEHFVTSMIKADGQFLAFFERPIAGTLGVITLLLWLLP-L 485 Query: 489 VGPLLRRR 496 L+RR+ Sbjct: 486 ALKLVRRK 493 Lambda K H 0.325 0.144 0.425 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: 760 Number of extensions: 56 Number of successful extensions: 4 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: 508 Length of database: 498 Length adjustment: 34 Effective length of query: 474 Effective length of database: 464 Effective search space: 219936 Effective search space used: 219936 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: 52 (24.6 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