Align Tricarboxylic transport TctA (characterized, see rationale)
to candidate SM_b20769 SM_b20769 hypothetical protein
Query= uniprot:E4PJQ9 (508 letters) >FitnessBrowser__Smeli:SM_b20769 Length = 512 Score = 369 bits (948), Expect = e-106 Identities = 191/505 (37%), Positives = 313/505 (61%), Gaps = 8/505 (1%) Query: 1 METLGFLMDGFAVALTPYNLMFALFGAFVGTLIGCLPGLGPANGVAILIPLAFTLGLPPE 60 ME +G L+DGF L+ +++ + G +G L+G LPGLG NGV++L+PL F++ P Sbjct: 1 MENIGLLIDGFGHILSWNHILLMIVGVTLGILVGVLPGLGAPNGVSLLLPLTFSMD--PI 58 Query: 61 TAMILLTAVYAGAMYGGRISSILLNIPGDEPAMMTCLDGYPMAQKGRAADALAVSAIASF 120 +A+ILL+ +Y GA++GG +SIL NIPG+ ++ T DGYPMA+ G A+ AL ++ +++ Sbjct: 59 SAIILLSCMYWGALFGGSTTSILFNIPGEPSSVATTFDGYPMARAGHASRALTLAFVSAG 118 Query: 121 AGGLIGTIGLIMLAPVLAKFALTFGPAEYFALFLLAFATLGGITGKNPVKTVVAATLGIM 180 G L G + + +L+ +A FAL F EYFA++ LAFA+ + ++P KT+V+ LG Sbjct: 119 LGALAGVVMITLLSGWVANFALKFSSPEYFAVYFLAFASFISMGAQSPFKTLVSMMLGFA 178 Query: 181 ISTVGIDISTGTQRYTFGVLELYEGIDFILAIVGLFAISELLFFVES--RMGRGRDKMNV 238 ++++G+D +G R TF + EL +G+ F++A++GLF I ELL E R + ++ + Sbjct: 179 LASIGMDTISGNLRLTFDIPELIKGVSFLIAVMGLFGIGELLLTTEEGLRFEGIKARVRL 238 Query: 239 GKLTLTMKELVMTIPTQLRGGVLGFISGVLPGAGASLGSFISYTLEKQVVGKKGKFGEGD 298 ++ T+ E+ T R ++G G+ P AG + SF+SY + ++ K FG+GD Sbjct: 239 SEIGRTLIEIPRYWLTIARSTIIGIWMGITP-AGPTAASFMSYGVARRSARDKSMFGKGD 297 Query: 299 IRGVVAPEAGNNGASSGALVPMLTLGVPGSGTTAVLLAMLISLNITPGPLMFTQNADIVW 358 RG+VAPE ++ A + AL+PML LGVPGS T AV++ L+ +TPGP++FT D VW Sbjct: 298 PRGIVAPETADHSAGTSALLPMLALGVPGSATAAVMMGGLMIWGLTPGPMLFTDRPDFVW 357 Query: 359 GVIAALLIGNVLLLVLNIPLVGFFVKLLSVPPMYLLPIVTMVAFVGIYSISHSTFDLYFM 418 G+IA++ +GNV+ + L I V + +L VP + PI+ V F G Y +++S D++ + Sbjct: 358 GLIASMYLGNVVAVFLVIATVPLYASILRVPFSIIGPIIVAVIFSGAYQVANSVSDIFMV 417 Query: 419 VAFGVAGYFLRKLEIPLVPIILGLLLGPEMEKNLGHALVLSDGEWSVLWASPLAMGLWIV 478 + FG+ GY +KL+ PL P++L ++LG + E ++++S G + W++ L L V Sbjct: 418 IGFGLLGYVFKKLDYPLAPLVLAMVLGDKAEDAFRQSMLMSGGSLDIFWSNGLVSALMAV 477 Query: 479 AGLGLILP---YLVGPLLRRRMNAA 500 A L+ P +L+G L +R+ A Sbjct: 478 ALALLLSPLFFWLIGTLRKRKNEVA 502 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: 723 Number of extensions: 42 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: 512 Length adjustment: 34 Effective length of query: 474 Effective length of database: 478 Effective search space: 226572 Effective search space used: 226572 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