Align Tricarboxylic transport TctA (characterized, see rationale)
to candidate AZOBR_RS23320 AZOBR_RS23320 C4-dicarboxylate ABC transporter permease
Query= uniprot:E4PJQ9 (508 letters) >FitnessBrowser__azobra:AZOBR_RS23320 Length = 500 Score = 266 bits (679), Expect = 2e-75 Identities = 156/485 (32%), Positives = 259/485 (53%), Gaps = 12/485 (2%) Query: 7 LMDGFAVALTPYNLMFALFGAFVGTLIGCLPGLGPANGVAILIPLAFTLGLPPETAMILL 66 L D V L + L+ + A G ++G +PGL A+L+P+ + P A I+ Sbjct: 4 LTDVLGVLLDVHLLLVIVASAIYGLVLGAIPGLTALMATALLVPVVMFMEPVPAIAAIIT 63 Query: 67 TAVYAGAMYGGRISSILLNIPGDEPAMMTCLDGYPMAQKGRAADALAVSAIASFAGGLIG 126 ++ A A++ G I L+ +PG + D Y + ++G+A +L +S GGL+ Sbjct: 64 SS--AMAIFAGDIPGALMRMPGTPASAAYTDDAYSLTREGKAGLSLGAGLFSSVLGGLLS 121 Query: 127 TIGLIMLAPVLAKFALTFGPAEYFALFLLAFATLGGITGKNPVKTVVAATLGIMISTVGI 186 + L + AP LA+ AL F EYF L +L + + G + +K V + G+ +ST+G+ Sbjct: 122 ALVLTLAAPNLAELALQFSSVEYFWLAVLGLSCATFVGGSSLLKGVASLLFGLGLSTIGM 181 Query: 187 DISTGTQRYTFGVLELYEGIDFILAIVGLFAISELLFFVE-SRMGRGRDKMNVGKLTLTM 245 D +GT R+TFGV L G+ I ++G+FA+SELL V G R + VG ++ M Sbjct: 182 DPVSGTPRFTFGVTNLLGGLGLIPLLIGVFAVSELLRTVTLPPTGERRAQPAVGSVSAGM 241 Query: 246 KELVMTIPTQ-LRGGVLGFISGVLPGAGASLGSFISYTLEKQVV-GKKGKFGEGDIRGVV 303 L+ + LRG LG + G LPGAGA + ++ISY + ++ GK + + +V Sbjct: 242 GRLMWRHRREVLRGSTLGTLVGALPGAGADIAAWISYAVTRRSQKGKDPNALDQKVERLV 301 Query: 304 APEAGNNGASSGALVPMLTLGVPGSGTTAVLLAMLISLNITPGPLMFTQNADIVWGVIAA 363 + A NN A GA +P G+PG TA++++++ + PGP +F N ++ + A Sbjct: 302 SAGAANNAALGGAYIPATVFGIPGDAITAIVISVMFLKGLNPGPTIFLNNPTAIYSIFAI 361 Query: 364 LLIGNVLLLVLNIPLVGFFVKLLSVPPMYLLPIVTMVAFVGIYSISHSTFDLYFMVAFGV 423 + N+L++ L I + F +L VP YL PI+ + VG +S+ ++ F + + G+ Sbjct: 362 FFVANLLMIPLGILCIRTFGLILKVPTAYLTPIILLFCIVGAFSVENTLFAVGIIAIVGL 421 Query: 424 AGYFLRKLEIPLVPIILGLLLGPEMEKNLGHALVLSDGEWSVLWASPLA-------MGLW 476 GYF+ +IP+ P +LGL+LGP +E+ +++ S GE SV + PLA +G W Sbjct: 422 LGYFMEANDIPMAPAVLGLILGPVIEQTFMTSMLKSGGEVSVFFDRPLAIALAVVTLGSW 481 Query: 477 IVAGL 481 +AG+ Sbjct: 482 ALAGV 486 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: 733 Number of extensions: 49 Number of successful extensions: 6 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: 508 Length of database: 500 Length adjustment: 34 Effective length of query: 474 Effective length of database: 466 Effective search space: 220884 Effective search space used: 220884 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