Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate SMc02337 SMc02337 ABC transporter ATP-binding protein
Query= uniprot:B2SYR5 (512 letters) >FitnessBrowser__Smeli:SMc02337 Length = 501 Score = 395 bits (1014), Expect = e-114 Identities = 216/499 (43%), Positives = 314/499 (62%), Gaps = 7/499 (1%) Query: 1 MSATLRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGR 60 M+ + I K F GV+AL GV FD+ G+VH L+GENGAGKSTL+++L GE +P SG Sbjct: 1 MTVLVSLSGISKNFSGVQALKGVDFDLRAGEVHALVGENGAGKSTLMRVLAGEMKPTSGT 60 Query: 61 VMIDGNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLPNSLGWVNKREAKRF 120 V I G ++ + + GI+VIHQEL PDLTVAEN+ LG+LP VN R ++ Sbjct: 61 VSIHGETMQHSGPRGAAGRGISVIHQELALAPDLTVAENIFLGRLPRI---VNHRRLRKA 117 Query: 121 VRERLEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLF 180 E LE +G +DP +L++A +Q+VEI KAL AR+I DEPT+ L++ + E L Sbjct: 118 ASEILERLGFDIDPAIHAGRLTVAHQQVVEIAKALSNRARIIVFDEPTAVLANTDAERLL 177 Query: 181 KLVRDLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMVGR 240 ++R+LRA +YISHR++E+++L D T+ +DG + + T D +++ MVGR Sbjct: 178 AIIRELRAGGTGAVYISHRLNEVFDLSDRITVMKDGSHVETLET-SATDVDAVIARMVGR 236 Query: 241 EISDIY-NYSARPLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLV 299 ++S ++ + + R GEV + + + SF VR GE+VG GLVG+GR+E+ LV Sbjct: 237 QMSALFPSKAGRVPGEVVVRVRNVSRGRKVRDVSFSVRAGEVVGLGGLVGSGRTEVARLV 296 Query: 300 YGADHKKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRH 359 +GAD G + L+GKP+ + S EA+R I L PEDRK++G++ A + N ++ R Sbjct: 297 FGADKMDSGTVELNGKPLHLSSPREAVRARIGLVPEDRKQQGVILDAPIRINTTLAKIRS 356 Query: 360 YLRVGMFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVV 419 R+G FLD KE + A +++K S + LSGGNQQK L++W D ++ Sbjct: 357 ISRLG-FLDAGKERQVAVALGAEMRLKASSVDAPVSSLSGGNQQKVALAKWF-HADCDLL 414 Query: 420 ILDEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGEL 479 ILDEPTRG+DVGAK EIYN+I LA+ G AI++ISSE E+ G+ DR++VM +G I GEL Sbjct: 415 ILDEPTRGVDVGAKGEIYNLINDLAKAGKAILVISSEHQELFGICDRVLVMAEGAIVGEL 474 Query: 480 TRKDATEQSVLSLALPQSS 498 T TEQ +L+LA+ +S+ Sbjct: 475 TESKFTEQQLLTLAMTRSA 493 Score = 60.8 bits (146), Expect = 1e-13 Identities = 57/242 (23%), Positives = 105/242 (43%), Gaps = 11/242 (4%) Query: 260 AKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGADHKKGGELLLDGKPIKV 319 +K G + F++R GE+ G GAG+S LM ++ G G + + G+ ++ Sbjct: 11 SKNFSGVQALKGVDFDLRAGEVHALVGENGAGKSTLMRVLAGEMKPTSGTVSIHGETMQH 70 Query: 320 RSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHYLRVGMFLDRKKEAETADRF 379 A GI + +E + TV+ENI + R+ ++ ++ + A Sbjct: 71 SGPRGAAGRGISVI---HQELALAPDLTVAENIFLG------RLPRIVNHRRLRKAASEI 121 Query: 380 IKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVILDEPTRGIDVGAKHEIYNV 439 ++ L R L+ +QQ +++ L+ ++++ DEPT + + + Sbjct: 122 LERLGFDIDPAIHAGR-LTVAHQQVVEIAKALSNR-ARIIVFDEPTAVLANTDAERLLAI 179 Query: 440 IYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELTRKDATEQSVLSLALPQSST 499 I +L G V IS L EV +SDRI VM+ G L +V++ + + + Sbjct: 180 IRELRAGGTGAVYISHRLNEVFDLSDRITVMKDGSHVETLETSATDVDAVIARMVGRQMS 239 Query: 500 AL 501 AL Sbjct: 240 AL 241 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: 628 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: 501 Length adjustment: 34 Effective length of query: 478 Effective length of database: 467 Effective search space: 223226 Effective search space used: 223226 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