Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate RR42_RS04800 RR42_RS04800 ABC transporter
Query= uniprot:B2SYR5 (512 letters) >FitnessBrowser__Cup4G11:RR42_RS04800 Length = 529 Score = 265 bits (676), Expect = 4e-75 Identities = 177/502 (35%), Positives = 269/502 (53%), Gaps = 23/502 (4%) Query: 5 LRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGRVMID 64 L +I K +PGV A D VS V G++H ++GENGAGKSTL+KI+ G +PD+G + + Sbjct: 9 LALAHISKRYPGVTANDDVSLVVAPGEIHAVLGENGAGKSTLMKIIFGAVKPDAGDMHFN 68 Query: 65 GNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLPNSL--------GWVNKRE 116 G + + GIA++ Q LTVAEN+ LG LP N ++ Sbjct: 69 GARAAIHNPHDARNLGIAMVFQHFSLFDTLTVAENIALG-LPRGSKTAAGSPHAGTNMKQ 127 Query: 117 AKRFVRERLEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRET 176 +RE G+ L+PN + LS+ +RQ VEI +ALL +++ LDEPTS L+ + Sbjct: 128 LAEQIRETALRYGLPLEPNRHVHTLSVGERQRVEIVRALLAKPQLLILDEPTSVLTPQAV 187 Query: 177 EVLFKLVRDLRADNRAMIYISHRMDEIYELCDACTIFRDGRKI-ASHPTLEGVTRDTIVS 235 + LF +R L A+ +++YISH++DEI ELC + T+ R GR P E ++ Sbjct: 188 QTLFITLRQLAAEGTSILYISHKLDEIRELCHSATVMRMGRVTGVCDPRQESAA--SLSR 245 Query: 236 EMVGREISDIYNYSARPLGEVRFAAKGI---EGHALAQP---ASFEVRRGEIVGFFGLVG 289 M+G E P G R A + + HA A S ++R GEIVG G+ G Sbjct: 246 LMIGGEPPREARVQTEP-GVCRLAVRELSLPRSHAFATELAGISLDLRAGEIVGIAGVSG 304 Query: 290 AGRSELMHLVYGADHKKGGE-LLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATV 348 G+ EL+ + G D + + + LD KP+ A + R G+ PE+R G V ++ Sbjct: 305 NGQQELLAALSGEDVRAARDAITLDNKPVGKLDARQRRRAGLAFVPEERLGRGAVPGMSL 364 Query: 349 SENINISCR-RHYLRVGMFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAIL 407 + NI +S + Y++ GM + K A A I L++K + LSGGN QK I+ Sbjct: 365 AANILLSHQSAPYVQRGM-ISPKAAAGLAQAVIARLRVKASGPHALAKSLSGGNLQKFIV 423 Query: 408 SRWLAEPDLKVVILDEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRI 467 R + E KV+I+ +PT G+DVGA +I+N + L GCA++++S EL E+ + DR+ Sbjct: 424 GREI-ESGPKVLIVAQPTWGVDVGAAAQIHNELLALKATGCALLVVSEELDELFAICDRL 482 Query: 468 VVMRQGRISGELTRKDATEQSV 489 V+ +GR+S + +DAT + V Sbjct: 483 HVIAKGRLSPSIPTRDATREQV 504 Score = 70.1 bits (170), Expect = 2e-16 Identities = 72/254 (28%), Positives = 115/254 (45%), Gaps = 22/254 (8%) Query: 249 SARPLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGADHKKGG 308 S P + +K G S V GEI G GAG+S LM +++GA G Sbjct: 4 STTPRLALAHISKRYPGVTANDDVSLVVAPGEIHAVLGENGAGKSTLMKIIFGAVKPDAG 63 Query: 309 ELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRH--------Y 360 ++ +G + + +A GI + + + TV+ENI + R + Sbjct: 64 DMHFNGARAAIHNPHDARNLGIAMVFQ---HFSLFDTLTVAENIALGLPRGSKTAAGSPH 120 Query: 361 LRVGMFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKA-ILSRWLAEPDLKVV 419 M ++ ETA R+ L+ P+R + LS G +Q+ I+ LA+P L + Sbjct: 121 AGTNMKQLAEQIRETALRYGLPLE---PNRH--VHTLSVGERQRVEIVRALLAKPQL--L 173 Query: 420 ILDEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGEL 479 ILDEPT + A ++ + QLA G +I+ IS +L E+ + VMR GR++G Sbjct: 174 ILDEPTSVLTPQAVQTLFITLRQLAAEGTSILYISHKLDEIRELCHSATVMRMGRVTGVC 233 Query: 480 TRKDATEQSVLSLA 493 D ++S SL+ Sbjct: 234 ---DPRQESAASLS 244 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: 618 Number of extensions: 35 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: 529 Length adjustment: 35 Effective length of query: 477 Effective length of database: 494 Effective search space: 235638 Effective search space used: 235638 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