Align ABC transporter related (characterized, see rationale)
to candidate Ac3H11_609 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)
Query= uniprot:A0KWY5 (499 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_609 Length = 505 Score = 325 bits (832), Expect = 3e-93 Identities = 183/503 (36%), Positives = 308/503 (61%), Gaps = 7/503 (1%) Query: 3 LILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGA--QSKDMGD 60 ++LE++ I K +PGV AL V+L++ AGE+HA++GENGAGKSTL+KV++G G Sbjct: 1 MLLEMRNIRKTFPGVVALNQVNLQVQAGEIHAIVGENGAGKSTLMKVLSGVYPHGSYSGQ 60 Query: 61 ILFLGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYAD 120 ILF G+ + F D++ GI ++QE+ LVP L++A+N+FLG E R G+I + ++ Sbjct: 61 ILFDGQEREFAGIRDSEHLGIIIIHQELALVPLLSIAENIFLGNETARHGVIDWMAAHSR 120 Query: 121 ARAVLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLF 180 A+A+L + L P+ + QQL+ IA+ ++ ++L+LDEPTASL+ + Q L Sbjct: 121 AQALLHKVGLGESPDTPVGQLGVGKQQLVEIAKALSRKVRLLILDEPTASLNENDSQALL 180 Query: 181 GILNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELP--QPKLIEAMLG 238 +L +LKA+G+ + I+H L+++ +++D ITVLR+G + E P + ++I+AM+G Sbjct: 181 DLLLELKAQGITCILISHKLNEISRVADAITVLRDGSTVQMLDCREGPVSEDRVIQAMVG 240 Query: 239 RSLQEQLVDKQEKE-RTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGR 297 R + ++ +Q + V S + ++ ++L V +G+ VG+AGL+G+GR Sbjct: 241 REMSDRYPQRQPQVGEIVFEVRNWRAHHPQRSDREHLKGIDLNVRRGEIVGIAGLMGAGR 300 Query: 298 SEVCNAVFGLDLVD--SGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRE 355 +E+ ++FG SG + L GQ +++S A+S G+A EDRK +G++ I+ Sbjct: 301 TELAMSIFGRSWGQRISGEVRLHGQPIDVSTVEKAVSHGLAYVTEDRKGNGLVLNEDIQF 360 Query: 356 NIILALQARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWL 415 N LA + + + + ++ +AQ + +KL+I D+ LSGGNQQKV+L++WL Sbjct: 361 NTSLANLPGVSFASVIDSGQEHRVAQDYREKLRIRCSGVDQKTLNLSGGNQQKVVLSKWL 420 Query: 416 AIEPILLVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRD 475 P +L+LDEPTRGID+GA EI LI L EG ++V SSE+ EL+ ++++ V+ + Sbjct: 421 FTSPEVLILDEPTRGIDVGAKYEIYTLIAQLAAEGKCVIVISSEMPELLGITDRIYVMNE 480 Query: 476 RYAVRELSGAELTSQHVMQAIAE 498 V E+ +E + + +M+AI + Sbjct: 481 GRFVAEMPTSEASQEKIMRAIVK 503 Score = 73.2 bits (178), Expect = 2e-17 Identities = 60/249 (24%), Positives = 120/249 (48%), Gaps = 11/249 (4%) Query: 3 LILELKQISKHYP---GVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQ--SKD 57 ++ E++ H+P + L+ + L + GE+ + G GAG++ L + G + Sbjct: 257 IVFEVRNWRAHHPQRSDREHLKGIDLNVRRGEIVGIAGLMGAGRTELAMSIFGRSWGQRI 316 Query: 58 MGDILFLGEPQHFNTPMDAQKAGISTVYQEVN---LVPNLTVAQNLFLGYEP--RRLGLI 112 G++ G+P +T A G++ V ++ LV N + N L P +I Sbjct: 317 SGEVRLHGQPIDVSTVEKAVSHGLAYVTEDRKGNGLVLNEDIQFNTSLANLPGVSFASVI 376 Query: 113 HFKKMYADARAVLTQFKLDID-VSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASL 171 + + A+ + ++ V + S QQ + +++ + S +VL+LDEPT + Sbjct: 377 DSGQEHRVAQDYREKLRIRCSGVDQKTLNLSGGNQQKVVLSKWLFTSPEVLILDEPTRGI 436 Query: 172 DAKEVQVLFGILNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPK 231 D ++ ++ QL A+G ++ I+ + ++ I+DRI V+ G+F+ E T+E Q K Sbjct: 437 DVGAKYEIYTLIAQLAAEGKCVIVISSEMPELLGITDRIYVMNEGRFVAEMPTSEASQEK 496 Query: 232 LIEAMLGRS 240 ++ A++ S Sbjct: 497 IMRAIVKAS 505 Lambda K H 0.319 0.136 0.377 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: 586 Number of extensions: 35 Number of successful extensions: 8 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: 499 Length of database: 505 Length adjustment: 34 Effective length of query: 465 Effective length of database: 471 Effective search space: 219015 Effective search space used: 219015 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 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