Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate 8501226 DvMF_1960 putrescine/spermidine ABC transporter ATPase protein (RefSeq)
Query= CharProtDB::CH_014279 (504 letters) >FitnessBrowser__Miya:8501226 Length = 399 Score = 112 bits (280), Expect = 2e-29 Identities = 86/277 (31%), Positives = 136/277 (49%), Gaps = 14/277 (5%) Query: 1 MQQSTPYLSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPT 60 M + + RG+ KTF AL I G+ L+G +G GK+T+L+++SG PT Sbjct: 1 MAEQDHIIELRGVTKTFEDTVALDSIDLTIRNGEFLTLLGPSGCGKTTILRLVSGFEQPT 60 Query: 61 TGSVVINGQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKGGIVNRSLL 120 +G V INGQ + + V ++Q L P MTV +N+ G L +G + + Sbjct: 61 SGEVRINGQVV---NRVPPEQRQVNTVFQNYALFPHMTVRDNVAFG-LKMQGVAADETAR 116 Query: 121 NYEAGLQLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREID 180 L++ HL + D + LS GQ Q V IA+A+ N ++ DEP S+L + Sbjct: 117 RVLDALRMVHL--ENFADRKPRQLSGGQQQRVAIARAVINNPLVLLLDEPFSALDFKLRK 174 Query: 181 NLFRVIRELRKE-GRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQA 239 + I+ L+++ G ++V+H EE FA+SD + V +GR + + + A Sbjct: 175 QMQLEIKHLQRQLGITFVFVTHDQEEAFAMSDRVVVMNEGRIEQIGAPKEIYEEPA--NM 232 Query: 240 MVGRDIGDIYGWQPRSYGEERLRLDAVKAPGVRTPIS 276 V R +GDI R + +RLD APG TP++ Sbjct: 233 YVARFVGDINALPGRI---DAVRLDWSAAPG--TPLA 264 Score = 72.4 bits (176), Expect = 3e-17 Identities = 58/210 (27%), Positives = 100/210 (47%), Gaps = 26/210 (12%) Query: 275 ISLAVRSGEIVGLFGLVGAGRSELMKGMFGGTQITAGQVYIDQQPIDIRKPSHAIAAGMM 334 I L +R+GE + L G G G++ +++ + G Q T+G+V I+ Q ++ R P Sbjct: 26 IDLTIRNGEFLTLLGPSGCGKTTILRLVSGFEQPTSGEVRINGQVVN-RVP--------- 75 Query: 335 LCPEDRKAE------GIIPVHSVRDNINISARRKHVLGGCVINNGWEENNADHHIRSLNI 388 PE R+ + P +VRDN+ + + V + +R +++ Sbjct: 76 --PEQRQVNTVFQNYALFPHMTVRDNVAFGLKMQGVAADETARRVLDA------LRMVHL 127 Query: 389 KTPGAEQLIMNLSGGNQQKAILGRWLSEEMKVILLDEPTRGIDVGAKHEIYNVIYALAAQ 448 + A++ LSGG QQ+ + R + V+LLDEP +D + ++ I L Q Sbjct: 128 EN-FADRKPRQLSGGQQQRVAIARAVINNPLVLLLDEPFSALDFKLRKQMQLEIKHLQRQ 186 Query: 449 -GVAVLFASSDLPEVLGVADRIVVMREGEI 477 G+ +F + D E ++DR+VVM EG I Sbjct: 187 LGITFVFVTHDQEEAFAMSDRVVVMNEGRI 216 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: 470 Number of extensions: 26 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: 399 Length adjustment: 33 Effective length of query: 471 Effective length of database: 366 Effective search space: 172386 Effective search space used: 172386 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: 51 (24.3 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