Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_013402887.1 CALHY_RS04860 ABC transporter ATP-binding protein
Query= uniprot:Q1MCU3 (247 letters) >NCBI__GCF_000166355.1:WP_013402887.1 Length = 503 Score = 102 bits (254), Expect = 1e-26 Identities = 69/223 (30%), Positives = 110/223 (49%), Gaps = 4/223 (1%) Query: 11 LLQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSVVF 70 +LQV + +GNI+A V + V KGE+ +++G NGAGKSTLM I G +G + F Sbjct: 4 ILQVKDISKRFGNIQANDNVCLDVKKGEVHAILGENGAGKSTLMNIIYGLYTPDSGEIYF 63 Query: 71 EGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGAGLDNLKHFAEDVEKIFTLF 130 EG+ + HE I + + P TV EN+ +G + ++ EK Sbjct: 64 EGQKLEVKGPHEAIEKGIGMVHQHFMLIPVFTVAENIVLGFEPKGFRFNVQEAEKKILEI 123 Query: 131 PR---LKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGIFEAIR 187 + L+ + G LS G QQ + I +A +LL+LDEP+ L P + +F+ I Sbjct: 124 SKKYNLEIDPKAKVGDLSVGMQQRVEILKAFYRDARLLILDEPTAMLTPQETRELFKIIN 183 Query: 188 KLNEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKE 230 L +A+G+++ + + +S R VM GK + + KE Sbjct: 184 NL-KAQGISILFISHKLDEVMEISDRVTVMRRGKTIKTLNTKE 225 Score = 72.8 bits (177), Expect = 1e-17 Identities = 59/232 (25%), Positives = 104/232 (44%), Gaps = 15/232 (6%) Query: 4 EVMTGQPLLQVNGVETYYGN-IRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQ 62 E G+ +L+V + N + + V V +GEI + G +G G++ L+ I G Sbjct: 248 EPRLGETVLKVENLSVKLKNGVEKVKDVSFEVRRGEIFGIAGVDGNGQNELVEAIVGLIS 307 Query: 63 ARTGSVVFEGRDITRMPTHEIARLRIAQSPEGRR---IFPRMTVLENLQM---------G 110 + TG ++F G++I +PT + IA P R+ + TV EN+ + Sbjct: 308 S-TGKIIFNGQEIQNLPTRKRYEKGIAYIPADRQQDGLVLNFTVAENIVLKRYYKNPYSN 366 Query: 111 AGLDNLKHFAEDVEKIFTLFPRLKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEP 170 G N K + +++ F + LSGG QQ + + R + P LL+ +P Sbjct: 367 RGFLNYKVITLEADRLIHEFDVRPPDYKLFAKNLSGGNQQKVILAREFSSSPDLLIAVQP 426 Query: 171 SLGLAPLIVKGIFEAIRKLNEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKV 222 + G+ ++ I + +L ++ G + LV L LS R VM +G++ Sbjct: 427 TRGMDVGAIEYIHRKLIELRDS-GKAILLVSLELDEILNLSDRIAVMYSGRI 477 Lambda K H 0.320 0.137 0.387 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: 280 Number of extensions: 13 Number of successful extensions: 5 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: 247 Length of database: 503 Length adjustment: 29 Effective length of query: 218 Effective length of database: 474 Effective search space: 103332 Effective search space used: 103332 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: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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