Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate PfGW456L13_7 ABC transporter ATP-binding protein
Query= CharProtDB::CH_014279 (504 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_7 Length = 521 Score = 238 bits (607), Expect = 4e-67 Identities = 160/496 (32%), Positives = 254/496 (51%), Gaps = 21/496 (4%) Query: 6 PYLSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVV 65 P L R I K +PG A I G++HAL+GENGAGKSTL+KI+ G +G V+ Sbjct: 12 PRLQLRRITKRYPGCLANDAIDLTIAPGEIHALLGENGAGKSTLMKIIYGVTHADSGEVI 71 Query: 66 INGQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKGGIVNRSLLNYEAG 125 GQ +S + A G+ +++Q L ++VA+NI L G L + Sbjct: 72 WQGQRVSLRNPAQARGLGIGMVFQHFSLFETLSVAQNIALAMGAAAG---TPKQLEPKIR 128 Query: 126 LQLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFRV 185 + GM ++P+ + LSIG+ Q VEI + L ++ +++ DEPTS L+ +E D+LF Sbjct: 129 EVSRRYGMTLEPERLVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEADDLFVT 188 Query: 186 IRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGRDI 245 +R L EG IL++SH++ E+ AL + TV + GR + D L + MVG + Sbjct: 189 LRRLAAEGCSILFISHKLGEVRALCHSATVLRGGRVAGHCVPAECSDQQ-LARLMVG-EA 246 Query: 246 GDIYGWQPRSYGEERLRLDAVKAPGVRTP---------ISLAVRSGEIVGLFGLVGAGRS 296 ++ P+ G + LD V+ P I L VR GEIVG+ G+ G G+ Sbjct: 247 AELIADYPKVTGGDAC-LD-VRGLSWHNPDPFGCSLANIDLEVRRGEIVGIAGVAGNGQD 304 Query: 297 ELMKGMFGGTQI---TAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRD 353 EL+ + G + + + ++P+ +P G+ P +R G +P S+ D Sbjct: 305 ELLALLSGEALLPRNASATIRFGKEPVAHLRPDARRQLGLAFVPAERLGHGAVPELSLAD 364 Query: 354 NINISARRKHVLGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRW 413 N ++A + ++ +I G E A+ IR +KTP ++ +LSGGN QK ILGR Sbjct: 365 NALLTAFQHGLVSNGLIQRGKVEALAEEIIRRFGVKTPDSQAPARSLSGGNLQKFILGRE 424 Query: 414 LSEEMKVILLDEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMR 473 + ++ ++++ PT G+DVGA I+ + AL G A+L S DL E+ ++DR+ + Sbjct: 425 ILQQPRLLVAAHPTWGVDVGAAATIHRALIALRDAGAAILVISEDLDELFQISDRLGALC 484 Query: 474 EGEIAGELLHEQADER 489 G ++ LH D R Sbjct: 485 GGRLSA--LHATVDTR 498 Score = 87.0 bits (214), Expect = 1e-21 Identities = 65/251 (25%), Positives = 123/251 (49%), Gaps = 20/251 (7%) Query: 260 RLRLDAVKAPG--VRTPISLAVRSGEIVGLFGLVGAGRSELMKGMFGGTQITAGQVYIDQ 317 +LR + PG I L + GEI L G GAG+S LMK ++G T +G+V Sbjct: 15 QLRRITKRYPGCLANDAIDLTIAPGEIHALLGENGAGKSTLMKIIYGVTHADSGEVIWQG 74 Query: 318 QPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVH-SVRDNINISARRKHVLGGCVINNGWEE 376 Q + +R P+ A G+ G++ H S+ + ++++ +G Sbjct: 75 QRVSLRNPAQARGLGI----------GMVFQHFSLFETLSVAQNIALAMGAAA----GTP 120 Query: 377 NNADHHIRSLNIK---TPGAEQLIMNLSGGNQQKAILGRWLSEEMKVILLDEPTRGIDVG 433 + IR ++ + T E+L+ +LS G +Q+ + R L +++++++LDEPT + Sbjct: 121 KQLEPKIREVSRRYGMTLEPERLVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQ 180 Query: 434 AKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAGELLHEQADERQALS 493 +++ + LAA+G ++LF S L EV + V+R G +AG + + ++Q Sbjct: 181 EADDLFVTLRRLAAEGCSILFISHKLGEVRALCHSATVLRGGRVAGHCVPAECSDQQLAR 240 Query: 494 LAMPKVSQAVA 504 L + + ++ +A Sbjct: 241 LMVGEAAELIA 251 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: 614 Number of extensions: 28 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: 504 Length of database: 521 Length adjustment: 35 Effective length of query: 469 Effective length of database: 486 Effective search space: 227934 Effective search space used: 227934 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