Align Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_084931811.1 HA51_RS03115 sugar ABC transporter ATP-binding protein
Query= uniprot:A0A166R419 (517 letters) >NCBI__GCF_002095475.1:WP_084931811.1 Length = 504 Score = 363 bits (932), Expect = e-105 Identities = 202/476 (42%), Positives = 299/476 (62%), Gaps = 8/476 (1%) Query: 24 LTGIDLTLMRGEVLALTGENGAGKSTLSKIIGGLVAPTTGQMRFQGRDYRPGSRSQAEEL 83 L G L + GEV AL GENGAGKSTL +++GG P +G + +G + A Sbjct: 21 LKGAQLQIRAGEVHALLGENGAGKSTLMRVLGGEHTPDSGTVYDKGEAVQIKGPKAAMAR 80 Query: 84 GIRMVMQELNLLPTLSVAENLFLDNLPSHGGWISRKQLRKAAIEAMAQVGLDAIDPDTLV 143 GI ++ QE+ L L+VAEN+FL +LP+ W +LR A + ++G + IDP V Sbjct: 81 GITLIHQEMALAQELTVAENIFLHDLPTFIAW---PKLRAKAANILRRLGFE-IDPAATV 136 Query: 144 GELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEMLFEQITRLQARGVSIIYISH 203 G+L + HQQ+VEIAR L D V++ DEPTA+L+ ++ L E I+ L++ GV+I+YISH Sbjct: 137 GDLSVAHQQIVEIARALSQDARVIVFDEPTAVLSTQDANRLLEIISDLRSVGVAIVYISH 196 Query: 204 RLEELARVAQRIAVLRDGNLVCVEPMANYNSEQLVTLMVGRELGEHI-DMGPRKIGAPAL 262 RL+E+ R+A R+ +++DG + E ++++ LMVGR + + D +G L Sbjct: 197 RLDEVFRIADRMTIMKDGQWIATESPQQTTLQEVIRLMVGRPVDQLFSDRATYGMGEEVL 256 Query: 263 TVKGLTRSDKVRDVSFEVRAGEIFGISGLIGAGRTELLRLIFGADTADSGTVALGASAQV 322 V+ L KVRDVSF VRAGE+ G+ GL+G+GRTE+ RLIFGAD DSG + L + Sbjct: 257 RVEKLNARRKVRDVSFSVRAGEVVGLGGLVGSGRTEVARLIFGADRCDSGDIYL--HGKK 314 Query: 323 VSIRSPADAVGHGIALITEDRKGEGLLLTQSISANIALGN-MPVISSGGFVNNGDEMSLA 381 VS+RSP AV GIAL+ EDRK +G++L I AN+ + N V++ GF+++ E + Sbjct: 315 VSLRSPQQAVKAGIALVPEDRKRQGVVLDMPIRANVTMANDKAVMAPLGFIHSSRETQVV 374 Query: 382 QRQINAMRIRSSSPTQLVSELSGGNQQKVVIGRWLERDCTVMLFDEPTRGIDVGAKFDIY 441 + MR++ + VS LSGGNQQKVV+ +W V++ DEPTRG+DVGAK +IY Sbjct: 375 SKLAQQMRLKCAGLHAPVSSLSGGNQQKVVLAKWFNLGGQVIILDEPTRGVDVGAKREIY 434 Query: 442 ALLGELTRQGKALVVVSSDLRELMLICDRIGVLSAGRLIDTFERDSWTQDDLLAAA 497 L+ EL +QG A+VV+SS+ EL +C+R+ V+S G + + D +++++LL+ A Sbjct: 435 QLIAELAQQGMAVVVISSEHIELFGLCNRVLVMSEGAICGELQPDDYSEENLLSMA 490 Score = 63.5 bits (153), Expect = 2e-14 Identities = 55/234 (23%), Positives = 112/234 (47%), Gaps = 10/234 (4%) Query: 15 IGKTYAQPVLTGIDLTLMRGEVLALTGENGAGKSTLSKIIGGLVAPTTGQMRFQGRDYRP 74 + K A+ + + ++ GEV+ L G G+G++ ++++I G +G + G+ Sbjct: 258 VEKLNARRKVRDVSFSVRAGEVVGLGGLVGSGRTEVARLIFGADRCDSGDIYLHGKKVSL 317 Query: 75 GSRSQAEELGIRMVMQE---LNLLPTLSVAENLFLDN---LPSHGGWISRKQLRKAAIEA 128 S QA + GI +V ++ ++ + + N+ + N + + G+I + + + Sbjct: 318 RSPQQAVKAGIALVPEDRKRQGVVLDMPIRANVTMANDKAVMAPLGFIHSSRETQVVSKL 377 Query: 129 MAQVGLDAIDPDTLVGELGIGHQQMVEIAR--NLIGDCHVLILDEPTAMLTAREVEMLFE 186 Q+ L V L G+QQ V +A+ NL G V+ILDEPT + +++ Sbjct: 378 AQQMRLKCAGLHAPVSSLSGGNQQKVVLAKWFNLGG--QVIILDEPTRGVDVGAKREIYQ 435 Query: 187 QITRLQARGVSIIYISHRLEELARVAQRIAVLRDGNLVCVEPMANYNSEQLVTL 240 I L +G++++ IS EL + R+ V+ +G + +Y+ E L+++ Sbjct: 436 LIAELAQQGMAVVVISSEHIELFGLCNRVLVMSEGAICGELQPDDYSEENLLSM 489 Lambda K H 0.319 0.137 0.384 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: 607 Number of extensions: 35 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 517 Length of database: 504 Length adjustment: 35 Effective length of query: 482 Effective length of database: 469 Effective search space: 226058 Effective search space used: 226058 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 52 (24.6 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