Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate WP_022530418.1 L248_RS11555 sugar ABC transporter ATP-binding protein
Query= uniprot:B2SYR5 (512 letters) >NCBI__GCF_000469325.1:WP_022530418.1 Length = 508 Score = 337 bits (864), Expect = 6e-97 Identities = 189/494 (38%), Positives = 294/494 (59%), Gaps = 12/494 (2%) Query: 5 LRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGRVMID 64 L +I K FPGV+ALD V D+ G+VH LMGENGAGKSTL+K++ G Y+ SG V + Sbjct: 14 LSMRHIAKYFPGVKALDDVQLDLRAGEVHALMGENGAGKSTLIKVMTGVYERTSGTVTLH 73 Query: 65 GNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLPNSLGWVNKREAKRFVRER 124 G ++ + + GI+ ++QE+ P+L+VAEN+ +G+ P G ++ + Sbjct: 74 GQDINPKTPQEAQDLGISTVYQEVNLCPNLSVAENVYIGRQPMRFGQIDWHRMNADAVKL 133 Query: 125 LEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLFKLVR 184 LE++ + +D L S++ +QM+ I +A+ +A V+ LDEPTSSL E LF ++R Sbjct: 134 LESLDIHVDVTKTLDSYSVSVQQMIAIARAVDMSAGVLILDEPTSSLDSNEVAQLFAIIR 193 Query: 185 DLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMVGREISD 244 LR N A+++++H MD++Y + D T+ R+GR I + + D +V++M+G++ D Sbjct: 194 HLRDQNMAILFVTHFMDQVYAISDRITVLRNGRYIGEYLAKDLPELD-LVTKMIGQKFVD 252 Query: 245 IYNYSARP---LGEVRFA-AKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVY 300 + RP VRF + I L S VR GE++G GL+G+GR+E+ L++ Sbjct: 253 ANTQAHRPSKDYSTVRFVRMEDISKRGLVHDFSMAVRAGEVLGLAGLLGSGRTEVAELLF 312 Query: 301 GADHKKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINIS--CRR 358 G H G + + +K + +A+ + C EDRK GIV ++ ENI +S ++ Sbjct: 313 GVTHFDDGVIYVGNDEVKRMNPRKALADQLGYCSEDRKVSGIVGDLSIRENIMLSLQAKK 372 Query: 359 HYLRVGMFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKV 418 R+ + KK+ E A ++I LL IKTPS +KI LSGGNQQK +L+RWLA D K+ Sbjct: 373 GLRRIPL----KKQQEVAQKYIDLLDIKTPSMEKKIGDLSGGNQQKVLLARWLA-TDPKL 427 Query: 419 VILDEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGE 478 +ILDEPTRGID+ K EI N+I +L+ +G AI+ ISSE E++ DRI+V+R GE Sbjct: 428 LILDEPTRGIDINTKREIENLIVKLSRQGMAIIFISSEYEEMVRTCDRIIVLRDRHAVGE 487 Query: 479 LTRKDATEQSVLSL 492 LT ++ +++ + Sbjct: 488 LTDNQISQDNIMKV 501 Score = 79.7 bits (195), Expect = 2e-19 Identities = 65/241 (26%), Positives = 113/241 (46%), Gaps = 8/241 (3%) Query: 256 VRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGADHKKGGELLLDGK 315 +R AK G ++R GE+ G GAG+S L+ ++ G + G + L G+ Sbjct: 16 MRHIAKYFPGVKALDDVQLDLRAGEVHALMGENGAGKSTLIKVMTGVYERTSGTVTLHGQ 75 Query: 316 PIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHYLRVGMFLDRKKEAET 375 I ++ EA GI + E + +V+EN+ I R +R G +D + Sbjct: 76 DINPKTPQEAQDLGISTVYQ---EVNLCPNLSVAENVYIG--RQPMRFGQ-IDWHRMNAD 129 Query: 376 ADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVILDEPTRGIDVGAKHE 435 A + ++ L I + + S QQ ++R + V+ILDEPT +D + Sbjct: 130 AVKLLESLDIHVDVTKTLDSY-SVSVQQMIAIAR-AVDMSAGVLILDEPTSSLDSNEVAQ 187 Query: 436 IYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELTRKDATEQSVLSLALP 495 ++ +I L ++ AI+ ++ + +V +SDRI V+R GR GE KD E +++ + Sbjct: 188 LFAIIRHLRDQNMAILFVTHFMDQVYAISDRITVLRNGRYIGEYLAKDLPELDLVTKMIG 247 Query: 496 Q 496 Q Sbjct: 248 Q 248 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: 593 Number of extensions: 31 Number of successful extensions: 9 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: 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 24 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