Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate SM_b20507 SM_b20507 L-arabinose transporter ATP-binding protein
Query= uniprot:B2SYR5 (512 letters) >FitnessBrowser__Smeli:SM_b20507 Length = 508 Score = 538 bits (1387), Expect = e-157 Identities = 271/498 (54%), Positives = 364/498 (73%), Gaps = 1/498 (0%) Query: 1 MSATLRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGR 60 M L F +I K +PGV+AL VSF V G VHGLMGENGAGKSTL+++L G+ D+G Sbjct: 1 MQDFLEFQSISKGYPGVQALSEVSFSVRKGAVHGLMGENGAGKSTLIRVLSGDQAADTGE 60 Query: 61 VMIDGNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLPNSLGWVNKREAKRF 120 + I+G + S + AG+ VIHQELQ VP+LTVAENL LG+ P G +++R+ R Sbjct: 61 IRINGEPQHYRSVRDAFNAGVIVIHQELQLVPELTVAENLWLGRFPGKAGVIDRRQLIRV 120 Query: 121 VRERLEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLF 180 V +RL +G+ +DP AK+ LSI +RQMVEI KA++ +ARVIALDEPTSSLS RE+E+LF Sbjct: 121 VSDRLAEIGIDVDPEAKVASLSIGERQMVEIAKAVMTDARVIALDEPTSSLSSRESEILF 180 Query: 181 KLVRDLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMVGR 240 L+ LR++ ++Y+SHR+DEI+ LC++ T+ RDGR A HP + V R+ I++EMVGR Sbjct: 181 ALIDRLRSNGTVILYVSHRLDEIFRLCNSLTVLRDGRLAAHHPDISKVGREQIIAEMVGR 240 Query: 241 EISDIYNYSARPLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVY 300 EIS+I+ + AR LG R + + G L QP SF VR GEI+GFFGL+GAGRSE+ LVY Sbjct: 241 EISNIWGWRARTLGAARLTVERVSGANLPQPISFTVRAGEILGFFGLIGAGRSEMARLVY 300 Query: 301 GADHKKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHY 360 GAD ++ G++L+DG + S +IR G+VLCPEDRK +GIV ++ EN+ IS RRH+ Sbjct: 301 GADRRRQGKVLVDGLAVPADSPRLSIRAGVVLCPEDRKFDGIVQGRSIEENMAISSRRHF 360 Query: 361 LRVGMFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVI 420 G+ +D+ KEAE A+RFI L+++TPSR Q I LSGGNQQK IL RWL+E +KV++ Sbjct: 361 SPFGV-VDKGKEAELAERFIAKLRVRTPSRHQDIVNLSGGNQQKVILGRWLSEEGVKVLL 419 Query: 421 LDEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELT 480 +DEPTRGIDVGAK EIY ++Y+LA +G AIV+ISSELPEV+G++DRI+VM +GRI+ E+ Sbjct: 420 IDEPTRGIDVGAKSEIYEILYELAAQGMAIVVISSELPEVMGIADRILVMCEGRIAAEID 479 Query: 481 RKDATEQSVLSLALPQSS 498 R D E +L+ ALP +S Sbjct: 480 RSDFDEHRILAAALPDAS 497 Lambda K H 0.320 0.136 0.385 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: 729 Number of extensions: 29 Number of successful extensions: 6 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: 512 Length of database: 508 Length adjustment: 34 Effective length of query: 478 Effective length of database: 474 Effective search space: 226572 Effective search space used: 226572 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