Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate 3609459 Dshi_2843 ABC transporter related (RefSeq)
Query= CharProtDB::CH_014279 (504 letters) >FitnessBrowser__Dino:3609459 Length = 548 Score = 275 bits (702), Expect = 4e-78 Identities = 176/508 (34%), Positives = 274/508 (53%), Gaps = 17/508 (3%) Query: 6 PYLSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVV 65 P + RGI K F V+A DIS G +H ++GENGAGKSTL+ IL G Y G + Sbjct: 24 PAIELRGISKAFGPVQANKDISIRVMPGTIHGIIGENGAGKSTLMSILYGFYKADAGEIF 83 Query: 66 INGQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKGGIVNRSLLNYEAG 125 I GQ+ D+ AA+ AG+ +++Q LV TV EN+ LG +G ++ SL Sbjct: 84 IKGQKTEIPDSQAAIRAGIGMVFQHFKLVENFTVLENVVLG--AEEGALLRPSLAKARKL 141 Query: 126 LQ--LKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLF 183 L+ + +++ PD ++ LS+G Q VEI KAL R A I+ DEPT L+ E D+LF Sbjct: 142 LRELSEEYELNVAPDALIEDLSVGHQQRVEILKALYRKADILILDEPTGVLTPAEADHLF 201 Query: 184 RVIRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGR 243 R++ L+ EG+ I+ ++H++ EI +D ++V + G T + L + MVGR Sbjct: 202 RILEGLKAEGKTIILITHKLREIMETTDTVSVMRRGEMTAT-VKTADTSPEQLAELMVGR 260 Query: 244 DIGDIYGWQPRSYGEERLRLD---AVKAPGVR--TPISLAVRSGEIVGLFGLVGAGRSEL 298 + P G L +D V GV ISL VR+GE++G+ G+ G G+SEL Sbjct: 261 KVLLRVDKTPAQPGAPILTVDDLRVVDDQGVERVKGISLQVRAGEVLGIAGVAGNGQSEL 320 Query: 299 MKGMFGGTQITAGQVYIDQQPIDIR-KPSHA---IAAGMMLCPEDRKAEGIIPVHSVRDN 354 ++ + GG + G+V + Q ID+ K S+ A G+ PEDR+AEG+I + +N Sbjct: 321 LE-VLGGMRPATGRVTVSGQQIDLTGKHSNGKTRRAQGIAHVPEDRQAEGLIMDYHAWEN 379 Query: 355 INISARRKHVLG-GCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRW 413 + G +++N +A+ I +++ N SGGNQQK +L R Sbjct: 380 VAFGYHDDPAYNRGLLMDNRAVRADAEGKIARFDVRPADCWLAAKNFSGGNQQKIVLARE 439 Query: 414 LSEEMKVILLDEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMR 473 + +++L+ +PTRG+D+GA I+ I AL G A+L S +L E+L ++DR+ VM Sbjct: 440 IERNPELLLVGQPTRGVDIGAIEFIHQQIIALRDAGKAILLVSVELEEILSLSDRVAVMF 499 Query: 474 EGEIAGELLHEQADERQALSLAMPKVSQ 501 +G I GE + +E++ L L M +++ Sbjct: 500 DGRIMGERPAAETNEKE-LGLLMAGITE 526 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: 684 Number of extensions: 38 Number of successful extensions: 10 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 504 Length of database: 548 Length adjustment: 35 Effective length of query: 469 Effective length of database: 513 Effective search space: 240597 Effective search space used: 240597 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