Align The threonine uptake permease, PhtA (Sauer et al., 2005) (required for maximal growth in macrophages and Acanthamoeba castellanii) (characterized)
to candidate WP_012386295.1 BIND_RS17205 MFS transporter
Query= TCDB::Q5ZY33 (427 letters) >NCBI__GCF_000019845.1:WP_012386295.1 Length = 441 Score = 175 bits (443), Expect = 3e-48 Identities = 126/409 (30%), Positives = 186/409 (45%), Gaps = 20/409 (4%) Query: 19 WLVWGLAAAFYFSDYLARVAPGVMHRYLQMDFGINEAGFGILTASFYVPYILMQIPVGLT 78 +L W L A FYF Y R APGVM L +G N G + +++Y+ Y +M + G+ Sbjct: 28 FLAWLLCAIFYFYQYAVRSAPGVMQEQLTQAWGGNH--IGAMISAYYIAYAVMALLAGVL 85 Query: 79 VDRLSIRWLLTIMSLVTAFGCCVFGLADGLLTAS-IGRMLIGFSAAFAFICSLRLATSWF 137 +DR + V G VF A G +A IG +L A FAFI S +A + Sbjct: 86 LDRYGAHATIPAGIAVVGIGSVVF--AQGSESAGMIGFVLQAIGAIFAFIGSSYVAARYL 143 Query: 138 PPTMLGLLSGLTQALGMLGAAAGEAPVSFLVSNVG-----WRHSMLIIAFLFIALSGLLY 192 P +ML + G TQ LGM GAA G PV FL+ G W+H L A L L+ + Sbjct: 144 PASMLAIFVGFTQCLGMAGAAFGSKPVQFLIDPTGSFHIAWQHVWLGFAVLGFVLAAATW 203 Query: 193 QFVQDKPGEHRNEIRSVNRISILDSLKIILSNKQTWLNAMYAGFLFGPTAVIGEAIGPAY 252 + G+ +++ S L + + SN Q+W M G LF PT + G Sbjct: 204 LVMPRDKGDSAEHHGTLSVASFLAPFRTVFSNPQSWFAGMIGGLLFVPTTIGALVWGTPM 263 Query: 253 LQFGRGLGAHAAAFATGLIFIGWGISGPLSGWISDKMGRRKPLMIISAVCGVILSSLFVF 312 L G AA ++ IGW I PL G+ISD++GRRKP++II + G++L S Sbjct: 264 LHQGEHTTMAFAASDVSMVPIGWVIGCPLLGYISDRIGRRKPVLIIGS--GILLVSCLTA 321 Query: 313 IP-EMSQTTAYILFFVFGLTNTGVAISYAVSTEIHDRSVVGTSIAFTNMTSIFVGALFQP 371 I + Y + + G+ + I ++V E + V GT+ N L P Sbjct: 322 ISVPVGVLPPYSVALLLGIASGAAMIPFSVIKEANIPQVKGTAAGVMNFLVFLTTGLMSP 381 Query: 372 LVGRIIDMVSGPRAYNVETLLLSDFQAGLKLLPLCSLVALILAFTVKET 420 +V ++ G + + + G+ L A+IL+F +KET Sbjct: 382 VVSALMRRDEGQMTMDTFRMAFTPLIGGVAL-------AIILSFFLKET 423 Lambda K H 0.329 0.143 0.438 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: 559 Number of extensions: 40 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: 427 Length of database: 441 Length adjustment: 32 Effective length of query: 395 Effective length of database: 409 Effective search space: 161555 Effective search space used: 161555 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 (21.8 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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