Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate WP_012042345.1 BBTA_RS09915 sugar ABC transporter ATP-binding protein
Query= uniprot:B2SYR5 (512 letters) >NCBI__GCF_000015165.1:WP_012042345.1 Length = 516 Score = 353 bits (907), Expect = e-102 Identities = 200/496 (40%), Positives = 306/496 (61%), Gaps = 12/496 (2%) Query: 5 LRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGRVMID 64 L + K F ++AL V F + G++H L+GENGAGKSTL+K++ G + D+G V + Sbjct: 15 LEIRGLTKSFGALKALQDVDFTLGEGEIHALLGENGAGKSTLIKVVTGVFARDAGTVRLA 74 Query: 65 GNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLPNSLGWVNKREAKRFVRER 124 G+E+ SA ++ AGIA ++QE+ +P+L+VA+NL LG+ P G V + E +R Sbjct: 75 GDEIAPRSAKDAVEAGIATVYQEVNLLPNLSVAQNLYLGRQPTRFGVVRQAEMRRRAHAL 134 Query: 125 LEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLFKLVR 184 L G+ +D A L S+A + + I +A+ +ARV+ LDEPT+SL E E+LF+++R Sbjct: 135 LLDYGLDIDVGAPLASYSVAVQHITAIARAVDLSARVLILDEPTASLDRHEVEILFRVMR 194 Query: 185 DLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMVGREISD 244 L AD ++++SH +D++YE+CD T+ R+GR I + + + R ++ M+GRE+++ Sbjct: 195 KLAADGIGIVFVSHFLDQVYEICDRVTVLRNGRLIGTR-DITDLPRLDLIRMMLGRELAE 253 Query: 245 IYNYSAR----PLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVY 300 + A EV + KG P E+RRGE+VG GL+G+GR+E LV+ Sbjct: 254 TTHERAASQPDTAREVCVSFKGFGKQGYVAPFDLELRRGEVVGLAGLLGSGRTETARLVF 313 Query: 301 GADHKKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHY 360 GA+ GE + GK +++ S +A G CPE+RK EGIVA TV ENI ++ + Sbjct: 314 GAERADSGEASVAGKAVRLNSPRDAAGLGFGYCPEERKTEGIVADLTVRENIVLALQ--- 370 Query: 361 LRVGMF--LDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKV 418 R G+ L R+++ E A R+I++L I+ P + I LSGGNQQKA+L+RWLA K+ Sbjct: 371 ARRGLHRPLSRREQDEIAMRYIRMLDIRPPDPERPIGLLSGGNQQKALLARWLATSP-KL 429 Query: 419 VILDEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGE 478 ++LDEPTRGIDVGA EI ++ L E+G A+++ISSEL E++ S+R+VV+R R E Sbjct: 430 LVLDEPTRGIDVGAHAEIIRLVRDLCEQGLALLVISSELDEIVTYSNRVVVLRD-RAHVE 488 Query: 479 LTRKDATEQSVLSLAL 494 + DA E S + A+ Sbjct: 489 ELKGDAVEVSSILAAI 504 Score = 75.5 bits (184), Expect = 4e-18 Identities = 73/269 (27%), Positives = 118/269 (43%), Gaps = 23/269 (8%) Query: 249 SARP-LGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGADHKKG 307 +ARP L E+R K Q F + GEI G GAG+S L+ +V G + Sbjct: 9 AARPSLLEIRGLTKSFGALKALQDVDFTLGEGEIHALLGENGAGKSTLIKVVTGVFARDA 68 Query: 308 GELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHYLRVGMFL 367 G + L G I RSA +A+ GI + E ++ +V++N+ + R R G+ Sbjct: 69 GTVRLAGDEIAPRSAKDAVEAGIATVYQ---EVNLLPNLSVAQNLYLG--RQPTRFGVV- 122 Query: 368 DRKKEAETADRFIKLL-------KIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVI 420 ++AE R LL + P + Q ++R + +V+I Sbjct: 123 ---RQAEMRRRAHALLLDYGLDIDVGAPLASYSVAV-----QHITAIAR-AVDLSARVLI 173 Query: 421 LDEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELT 480 LDEPT +D ++ V+ +LA G IV +S L +V + DR+ V+R GR+ G Sbjct: 174 LDEPTASLDRHEVEILFRVMRKLAADGIGIVFVSHFLDQVYEICDRVTVLRNGRLIGTRD 233 Query: 481 RKDATEQSVLSLALPQSSTALPGTQAAAQ 509 D ++ + L + +AA+Q Sbjct: 234 ITDLPRLDLIRMMLGRELAETTHERAASQ 262 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: 644 Number of extensions: 37 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 512 Length of database: 516 Length adjustment: 35 Effective length of query: 477 Effective length of database: 481 Effective search space: 229437 Effective search space used: 229437 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