Align Tricarboxylic transport TctA (characterized, see rationale)
to candidate AZOBR_RS22480 AZOBR_RS22480 tricarboxylate transporter
Query= uniprot:E4PJQ9 (508 letters) >FitnessBrowser__azobra:AZOBR_RS22480 Length = 508 Score = 397 bits (1021), Expect = e-115 Identities = 205/498 (41%), Positives = 314/498 (63%), Gaps = 6/498 (1%) Query: 1 METLGFLMDGFAVALTPYNLMFALFGAFVGTLIGCLPGLGPANGVAILIPLAFTLGLPPE 60 +E LG L+ GF V P N+ + G +G LIG LPGLG ANGVAIL+PL F++ P Sbjct: 1 LEALGSLIQGFGVLADPMNIAYMFIGITLGVLIGVLPGLGGANGVAILLPLTFSMS--PT 58 Query: 61 TAMILLTAVYAGAMYGGRISSILLNIPGDEPAMMTCLDGYPMAQKGRAADALAVSAIASF 120 +A+I+L+ +Y GA++GG I+S+L NIPG+ ++ T DG+PMAQKG A +AL + +SF Sbjct: 59 SAIIMLSCIYWGALFGGAITSVLFNIPGEPWSVATTFDGHPMAQKGHAGEALTAAFTSSF 118 Query: 121 AGGLIGTIGLIMLAPVLAKFALTFGPAEYFALFLLAFATLGGITGKNPVKTVVAATLGIM 180 G + + + LAPV+A FAL FGPAE+FA+ LL F + G+ ++P K + A LG Sbjct: 119 FGAFVAVLLITFLAPVIAGFALRFGPAEFFAVQLLTFCSFVGMGSESPFKVLCAMMLGFA 178 Query: 181 ISTVGIDISTGTQRYTFGVLELYEGIDFILAIVGLFAISELLFFVESRMG-RGRD-KMNV 238 ++ VG+D TG R TFG +EL G DF++A++GLF I E+L +E + +G+ K+N Sbjct: 179 LAAVGLDSVTGELRMTFGSVELLRGFDFLIAVIGLFGIGEILLTMEEGLAFKGKSAKINA 238 Query: 239 GKLTLTMKELVMTIPTQLRGGVLGFISGVLPGAGASLGSFISYTLEKQVVGKKGKFGEGD 298 + T K L T +RG ++G G+ PG GA+ SF+SY L K+ + FG G+ Sbjct: 239 KVVWETWKSLPRYWVTAIRGSIVGCWMGITPG-GATPASFMSYGLAKRFSRNRQNFGNGE 297 Query: 299 IRGVVAPEAGNNGASSGALVPMLTLGVPGSGTTAVLLAMLISLNITPGPLMFTQNADIVW 358 + GVVAPE + A + AL+PMLTLG+PGS T AVLL L+ + PGPL+F + + VW Sbjct: 298 MEGVVAPETAAHAAGTSALLPMLTLGIPGSPTAAVLLGGLLIWGLQPGPLLFIEQKEFVW 357 Query: 359 GVIAALLIGNVLLLVLNIPLVGFFVKLLSVPPMYLLPIVTMVAFVGIYSISHSTFDLYFM 418 G+IA++ +GN+ L++ + V F +L +P + P++ ++ VG Y++ ++ D+ M Sbjct: 358 GLIASMYLGNIAGLIVVLTTVPVFASILRIPFSIIAPVIVVICAVGAYTVHNAFLDIVMM 417 Query: 419 VAFGVAGYFLRKLEIPLVPIILGLLLGPEMEKNLGHALVLSDGEWSVLWASPLAMGLWIV 478 + FGV GY +KL PL P++L L+LG E + A+++S G+ ++ W++PL + + Sbjct: 418 LVFGVVGYVFKKLSYPLAPLVLALVLGDMAESSFRQAMLVSQGDLAIFWSNPLVGSIVTL 477 Query: 479 AGLGLILPYLVGPLLRRR 496 A + L P ++ LLR+R Sbjct: 478 ALVMLFWP-VISALLRKR 494 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: 794 Number of extensions: 53 Number of successful extensions: 5 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: 508 Length adjustment: 34 Effective length of query: 474 Effective length of database: 474 Effective search space: 224676 Effective search space used: 224676 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