Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate BPHYT_RS16930 BPHYT_RS16930 arabinose ABC transporter ATP-binding protein
Query= CharProtDB::CH_014279 (504 letters) >FitnessBrowser__BFirm:BPHYT_RS16930 Length = 512 Score = 516 bits (1329), Expect = e-151 Identities = 265/497 (53%), Positives = 350/497 (70%), Gaps = 1/497 (0%) Query: 8 LSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVVIN 67 L F IGK FPGV+AL +SFD GQVH LMGENGAGKSTLLKIL G Y P +G V+I+ Sbjct: 5 LRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGRVMID 64 Query: 68 GQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKGGIVNRSLLNYEAGLQ 127 G E+ F+ +++ AG+A+I+QEL VP++TVAEN+ LGQLP+ G VN+ + Sbjct: 65 GNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLPNSLGWVNKREAKRFVRER 124 Query: 128 LKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFRVIR 187 L+ +G+ +DP+ L+ LSI Q QMVEI KAL RNA++IA DEPTSSLS RE + LF+++R Sbjct: 125 LEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLFKLVR 184 Query: 188 ELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGRDIGD 247 +LR + R ++Y+SHRM+EI+ L DA T+F+DGR + + ++ V D +V MVGR+I D Sbjct: 185 DLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMVGREISD 244 Query: 248 IYGWQPRSYGEERLRLDAVKAPGVRTPISLAVRSGEIVGLFGLVGAGRSELMKGMFGGTQ 307 IY + R GE R ++ + P S VR GEIVG FGLVGAGRSELM ++G Sbjct: 245 IYNYSARPLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGADH 304 Query: 308 ITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINISARRKHVLGG 367 G++ +D +PI +R AI G++LCPEDRK EGI+ + +V +NINIS RR ++ G Sbjct: 305 KKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHYLRVG 364 Query: 368 CVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSE-EMKVILLDEP 426 ++ E AD I+ L IKTP Q I LSGGNQQKAIL RWL+E ++KV++LDEP Sbjct: 365 MFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVILDEP 424 Query: 427 TRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAGELLHEQA 486 TRGIDVGAKHEIYNVIY LA +G A++ SS+LPEVLGV+DRIVVMR+G I+GEL + A Sbjct: 425 TRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELTRKDA 484 Query: 487 DERQALSLAMPKVSQAV 503 E+ LSLA+P+ S A+ Sbjct: 485 TEQSVLSLALPQSSTAL 501 Score = 67.0 bits (162), Expect = 2e-15 Identities = 58/243 (23%), Positives = 104/243 (42%), Gaps = 8/243 (3%) Query: 6 PYLSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVV 65 P R K G SF+ G++ G GAG+S L+ ++ G G ++ Sbjct: 252 PLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGADHKKGGELL 311 Query: 66 INGQEMSFSDTTAALNAGVAII---YQELHLVPEMTVAENIYLGQLPH---KGGIVNRSL 119 ++G+ + A+ G+ + +E +V TV+ENI + H G ++R Sbjct: 312 LDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHYLRVGMFLDRKK 371 Query: 120 LNYEAGLQLKHLGMDI-DPDTPLKYLSIGQWQMVEIAKALAR-NAKIIAFDEPTSSLSAR 177 A +K L + +++LS G Q +++ LA + K++ DEPT + Sbjct: 372 EAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVILDEPTRGIDVG 431 Query: 178 EIDNLFRVIRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALV 237 ++ VI +L + G I+ +S + E+ +SD I V + GR T + L Sbjct: 432 AKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELTRKDATEQSVLS 491 Query: 238 QAM 240 A+ Sbjct: 492 LAL 494 Lambda K H 0.319 0.136 0.391 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: 726 Number of extensions: 32 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: 2 Length of query: 504 Length of database: 512 Length adjustment: 34 Effective length of query: 470 Effective length of database: 478 Effective search space: 224660 Effective search space used: 224660 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 (21.7 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