Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate Echvi_0300 Echvi_0300 gliding motility-associated ABC transporter ATP-binding subunit GldA
Query= uniprot:B2SYR5 (512 letters) >FitnessBrowser__Cola:Echvi_0300 Length = 305 Score = 101 bits (251), Expect = 4e-26 Identities = 83/257 (32%), Positives = 121/257 (47%), Gaps = 15/257 (5%) Query: 4 TLRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGRVMI 63 +L + K + RAL VSF GQV G +G NGAGKST +KI G PD G V++ Sbjct: 2 SLEVKELSKYYGQQRALKEVSFTAEKGQVLGFLGPNGAGKSTTMKIAAGYLLPDGGDVLV 61 Query: 64 DGNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLPNSLGWVNKREAKRFVRE 123 +G V S G H L ++ V E L L + ++AK + Sbjct: 62 NGVSVMDHPQEVSKMIGYLPEHNPLYL--EMYVREFL---SFMAGLYQLKGKKAKARIDG 116 Query: 124 RLEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLFKLV 183 +EA G+ + + K+ LS RQ V + KAL+ + VI LDEPTS L + + KL+ Sbjct: 117 VVEACGLGDEQHKKIGALSKGYRQRVGLAKALVHDPAVIILDEPTSGLDPNQLVDIRKLI 176 Query: 184 RDLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMVGREIS 243 + + A+ + ++ +H M E+ LC+ I G + S L + D SEMV Sbjct: 177 KSISAE-KTLVLSTHVMQEVEALCEKVVIIHQG-NVVSQDLLANLKSDN--SEMV----- 227 Query: 244 DIYNYSARPLGEVRFAA 260 +Y + L E FAA Sbjct: 228 -LYLETQERLREEWFAA 243 Score = 60.1 bits (144), Expect = 1e-13 Identities = 57/222 (25%), Positives = 104/222 (46%), Gaps = 16/222 (7%) Query: 255 EVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGADHKKGGELLLDG 314 EV+ +K + SF +G+++GF G GAG+S M + G GG++L++G Sbjct: 4 EVKELSKYYGQQRALKEVSFTAEKGQVLGFLGPNGAGKSTTMKIAAGYLLPDGGDVLVNG 63 Query: 315 KPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHYLRVGMFLDRKKEAE 374 + V + + I PE + V E ++ + L+ KK Sbjct: 64 --VSVMDHPQEVSKMIGYLPE---HNPLYLEMYVREFLSFMAGLYQLK------GKKAKA 112 Query: 375 TADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVILDEPTRGIDVGAKH 434 D ++ + + +KI LS G +Q+ L++ L D V+ILDEPT G+D Sbjct: 113 RIDGVVEACGL-GDEQHKKIGALSKGYRQRVGLAKALVH-DPAVIILDEPTSGLDPNQLV 170 Query: 435 EIYNVIYQL-AERGCAIVMISSELPEVLGVSDRIVVMRQGRI 475 +I +I + AE+ +V+ + + EV + +++V++ QG + Sbjct: 171 DIRKLIKSISAEK--TLVLSTHVMQEVEALCEKVVIIHQGNV 210 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: 309 Number of extensions: 22 Number of successful extensions: 4 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: 305 Length adjustment: 31 Effective length of query: 481 Effective length of database: 274 Effective search space: 131794 Effective search space used: 131794 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: 50 (23.9 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