Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate Pf1N1B4_1243 ABC transporter ATP-binding protein
Query= uniprot:B2SYR5 (512 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1243 Length = 521 Score = 234 bits (598), Expect = 4e-66 Identities = 151/481 (31%), Positives = 247/481 (51%), Gaps = 14/481 (2%) Query: 5 LRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGRVMID 64 L+ I K +PG A D + + G++H L+GENGAGKSTL+KI+ G DSG ++ Sbjct: 14 LQLRRISKRYPGCLANDAIDLSIAPGEIHALLGENGAGKSTLMKIIYGVTHADSGEMIWQ 73 Query: 65 GNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLPNSLGWVNKREAKRFVRER 124 G V + A + GI ++ Q L+VA+N+ L + + G + E K +RE Sbjct: 74 GQRVTMRNPAQARGLGIGMVFQHFSLFETLSVAQNIALA-MGAAAGTPKQLEPK--IREV 130 Query: 125 LEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLFKLVR 184 + G+AL+P + LSI +RQ VEI + L+++ R++ LDEPTS L+ +E + LF +R Sbjct: 131 SQRYGMALEPERLVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEADELFVTLR 190 Query: 185 DLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMVGREISD 244 L A+ ++++ISH++ E+ LC + T+ R GR +A H + + MVG Sbjct: 191 RLAAEGCSILFISHKLGEVRALCHSATVLRGGR-VAGHCVPAQCSDRQLAQLMVGEAAEL 249 Query: 245 IYNYSARPLGEVRFAAKGIEGH------ALAQPASFEVRRGEIVGFFGLVGAGRSELMHL 298 I +Y + + G+ H + F+VR GEIVG G+ G G+ EL+ L Sbjct: 250 ITDYPKVMGADAFLSVTGLSWHNPDPFGCSLKNIDFDVRSGEIVGVAGVAGNGQDELLAL 309 Query: 299 VYGAD---HKKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINIS 355 + G + + G+P+ + G+ P +R G V ++++N ++ Sbjct: 310 LSGEERLPRDDSATISFGGQPVAHLRPDARRKLGLAFVPAERLGHGAVPELSLADNALLT 369 Query: 356 CRRHYLRVGMFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPD 415 + L + R K A+ I+ +KTP R LSGGN QK IL R + + Sbjct: 370 AFQQGLVSHGLVQRGKVQALAEDIIRRFGVKTPDSLAPARSLSGGNLQKFILGREILQQP 429 Query: 416 LKVVILDEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRI 475 K+++ PT G+DVGA I+ + L + G AI++IS +L E+ + DR+ + G++ Sbjct: 430 -KLLVAAHPTWGVDVGAAATIHRALIALRDAGAAILVISEDLDELFQICDRLGALCGGQL 488 Query: 476 S 476 S Sbjct: 489 S 489 Score = 83.6 bits (205), Expect = 2e-20 Identities = 61/247 (24%), Positives = 116/247 (46%), Gaps = 11/247 (4%) Query: 252 PLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGADHKKGGELL 311 P ++R +K G + GEI G GAG+S LM ++YG H GE++ Sbjct: 12 PRLQLRRISKRYPGCLANDAIDLSIAPGEIHALLGENGAGKSTLMKIIYGVTHADSGEMI 71 Query: 312 LDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHYLRVGMFLDRKK 371 G+ + +R+ +A GI + + + +V++NI ++ +G K Sbjct: 72 WQGQRVTMRNPAQARGLGIGMVFQ---HFSLFETLSVAQNIALA-------MGAAAGTPK 121 Query: 372 EAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVILDEPTRGIDVG 431 + E R + + + LS G +Q+ + R L + D++++ILDEPT + Sbjct: 122 QLEPKIREVSQRYGMALEPERLVHSLSIGERQRVEIIRCLMQ-DIRLLILDEPTSVLTPQ 180 Query: 432 AKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELTRKDATEQSVLS 491 E++ + +LA GC+I+ IS +L EV + V+R GR++G +++ + Sbjct: 181 EADELFVTLRRLAAEGCSILFISHKLGEVRALCHSATVLRGGRVAGHCVPAQCSDRQLAQ 240 Query: 492 LALPQSS 498 L + +++ Sbjct: 241 LMVGEAA 247 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: 657 Number of extensions: 36 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: 521 Length adjustment: 35 Effective length of query: 477 Effective length of database: 486 Effective search space: 231822 Effective search space used: 231822 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