Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate WP_013402887.1 CALHY_RS04860 ABC transporter ATP-binding protein
Query= uniprot:D8IUY7 (241 letters) >NCBI__GCF_000166355.1:WP_013402887.1 Length = 503 Score = 98.2 bits (243), Expect = 3e-25 Identities = 64/214 (29%), Positives = 109/214 (50%), Gaps = 4/214 (1%) Query: 5 ILKVQQLSVAYGGIQAVKGIDLEVNEGELVTLIGANGAGKTTTLKAITGTLPASRVEGHI 64 IL+V+ +S +G IQA + L+V +GE+ ++G NGAGK+T + I G G I Sbjct: 4 ILQVKDISKRFGNIQANDNVCLDVKKGEVHAILGENGAGKSTLMNIIYGLYTPD--SGEI 61 Query: 65 EYLGQPLKGKKSFELVKDKLAMVPEGRGVFTRMSIQENLLMGAYTSDDKGQIAADIDKWF 124 + GQ L+ K E ++ + MV + + ++ EN+++G + + K Sbjct: 62 YFEGQKLEVKGPHEAIEKGIGMVHQHFMLIPVFTVAENIVLGFEPKGFRFNVQEAEKKIL 121 Query: 125 AVFPR--LKERAAQMAGTLSGGEQQMLAMARALMSHPKLLLLDEPSMGLSPIMVEKIFEV 182 + + L+ G LS G QQ + + +A +LL+LDEP+ L+P ++F++ Sbjct: 122 EISKKYNLEIDPKAKVGDLSVGMQQRVEILKAFYRDARLLILDEPTAMLTPQETRELFKI 181 Query: 183 IRNVSAQGITILLVEQNAKLALEAAHRGYVMESG 216 I N+ AQGI+IL + +E + R VM G Sbjct: 182 INNLKAQGISILFISHKLDEVMEISDRVTVMRRG 215 Score = 79.3 bits (194), Expect = 1e-19 Identities = 62/226 (27%), Positives = 103/226 (45%), Gaps = 15/226 (6%) Query: 5 ILKVQQLSVAY-GGIQAVKGIDLEVNEGELVTLIGANGAGKTTTLKAITGTLPASRVEGH 63 +LKV+ LSV G++ VK + EV GE+ + G +G G+ ++AI G + ++ G Sbjct: 255 VLKVENLSVKLKNGVEKVKDVSFEVRRGEIFGIAGVDGNGQNELVEAIVGLISST---GK 311 Query: 64 IEYLGQPLKGKKSFELVKDKLAMVPEGR---GVFTRMSIQENLLMGAYTSDDKGQ----- 115 I + GQ ++ + + + +A +P R G+ ++ EN+++ Y + Sbjct: 312 IIFNGQEIQNLPTRKRYEKGIAYIPADRQQDGLVLNFTVAENIVLKRYYKNPYSNRGFLN 371 Query: 116 ---IAADIDKWFAVFPRLKERAAQMAGTLSGGEQQMLAMARALMSHPKLLLLDEPSMGLS 172 I + D+ F A LSGG QQ + +AR S P LL+ +P+ G+ Sbjct: 372 YKVITLEADRLIHEFDVRPPDYKLFAKNLSGGNQQKVILAREFSSSPDLLIAVQPTRGMD 431 Query: 173 PIMVEKIFEVIRNVSAQGITILLVEQNAKLALEAAHRGYVMESGLI 218 +E I + + G ILLV L + R VM SG I Sbjct: 432 VGAIEYIHRKLIELRDSGKAILLVSLELDEILNLSDRIAVMYSGRI 477 Lambda K H 0.317 0.134 0.365 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: 253 Number of extensions: 17 Number of successful extensions: 4 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: 241 Length of database: 503 Length adjustment: 29 Effective length of query: 212 Effective length of database: 474 Effective search space: 100488 Effective search space used: 100488 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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