Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate 206505 DVU1070 branched chain amino acid ABC transporter, ATP-binding protein (TIGR)
Query= uniprot:B2SYR5 (512 letters) >FitnessBrowser__DvH:206505 Length = 524 Score = 270 bits (689), Expect = 1e-76 Identities = 169/497 (34%), Positives = 266/497 (53%), Gaps = 13/497 (2%) Query: 1 MSATLRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGR 60 ++ +R + IGK F VRA ++ D+ G++ L+GENGAGKSTL+ IL G D+G Sbjct: 31 VTPVVRLEGIGKSFGPVRANHDITLDIVPGRIKALLGENGAGKSTLMSILSGRLAQDTGI 90 Query: 61 VMIDGNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLPNSLGWVNKREAKRF 120 + +DG VRF S ++ AGI +++Q V +TVAEN+LLGQ S W++ R Sbjct: 91 IHVDGEAVRFRSPKDALKAGIGMVYQHFMLVDSMTVAENVLLGQ---SGAWLSPVHMSRV 147 Query: 121 VRERLEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLF 180 V E G+ +DP A++ LS+ +RQ VEI K L R++RV+ LDEPT+ L+ ETE LF Sbjct: 148 VAELAARYGLDIDPAARVCDLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPGETEQLF 207 Query: 181 KLVRDLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMVGR 240 + + + + +A+++ISH+M E+ L D I R G + E + + MVGR Sbjct: 208 EALHRMAENGKAIVFISHKMQEVLALADEIAILRRGEVVDEFHESEVPGEAELANRMVGR 267 Query: 241 EISDIYNYSARPL--GEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHL 298 E+ I +A PL G+ G+ G L + SFEVR+GE+ G+ G G+ EL+ Sbjct: 268 EV--ILEVAAEPLEPGDRVLHVDGLAGDGL-KGLSFEVRKGEVFAIAGVAGNGQRELVEC 324 Query: 299 VYGADHKKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRR 358 V G GE+ L G P + + G+ PEDR+ + +N ++ R Sbjct: 325 VTGLRRPAEGEVELLGIPWRQFFTKAPRQGGLAYIPEDRQGLATCLSLDLVDNFLLTARG 384 Query: 359 HYLRVGMFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSR-WLAEPDLK 417 + R G FLDRK A + ++ R LSGGN QK ++ R + +P L Sbjct: 385 CFTR-GPFLDRKSADAAARDILAEYNVQPGRAEAPARSLSGGNLQKLVVGREFYRKPSL- 442 Query: 418 VVILDEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISG 477 ++ + PT+G+D+ A E++ + ++ ++++S +L EVL ++DR+ VM +G G Sbjct: 443 -IVAENPTQGLDIAATEEVWARLLEVRSH-AGVLLVSGDLNEVLALADRVAVMYRGCFIG 500 Query: 478 ELTRKDATEQSVLSLAL 494 L R D + + L + Sbjct: 501 LLDRSDTNKVDAIGLMM 517 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: 639 Number of extensions: 44 Number of successful extensions: 9 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: 524 Length adjustment: 35 Effective length of query: 477 Effective length of database: 489 Effective search space: 233253 Effective search space used: 233253 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 Apr 09 2024. 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