Align High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale)
to candidate 7024900 Shewana3_2074 ABC transporter related (RefSeq)
Query= uniprot:A0A159ZWL6 (233 letters) >FitnessBrowser__ANA3:7024900 Length = 499 Score = 101 bits (252), Expect = 2e-26 Identities = 76/241 (31%), Positives = 119/241 (49%), Gaps = 15/241 (6%) Query: 1 MLQFENVSTFYGKIQALHSVNVEVRQGEIVTLIGANGAGKSTLLMTLCGSPQAHSGSIRY 60 +L+ + +S Y ++AL V++ + GE+ L+G NGAGKSTL+ + G+ G I + Sbjct: 4 ILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILF 63 Query: 61 MGEELVGQDSSHIMRKSIAVVPEGRRVFARLTVEENLAMG------GFFTDKGDYQEQMD 114 +GE + I+ V + + LTV +NL +G G K Y + Sbjct: 64 LGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYADAR- 122 Query: 115 KVLHLFPRLKERFTQRGGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFD 174 VL F +L + S QQ++AI R + K+L+LDEP+ L +Q +F Sbjct: 123 AVLTQF-KLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFG 181 Query: 175 IIEQLRKDGVTVFLVEQNANQALKIADRAYVLENGRVVMQGTGEAL---LTDPKVREAYL 231 I+ QL+ GV + + +Q +I+DR VL NG+ + GE L L PK+ EA L Sbjct: 182 ILNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFI----GEYLTAELPQPKLIEAML 237 Query: 232 G 232 G Sbjct: 238 G 238 Score = 73.6 bits (179), Expect = 7e-18 Identities = 67/247 (27%), Positives = 119/247 (48%), Gaps = 23/247 (9%) Query: 1 MLQFENVSTFYGKIQALHSVNVEVRQGEIVTLIGANGAGKSTLLMTLCGSPQAHSGSIRY 60 +L E+VS G IQ S+N+ V +G+ V L G G+G+S + + G SGSI Sbjct: 262 LLSLEDVSV-KGSIQ---SMNLTVPKGQAVGLAGLLGSGRSEVCNAVFGLDLVDSGSIHL 317 Query: 61 MGEELVGQDSSHIMRKSIAVVPEGRRV---FARLTVEENLAMG-----GFFTDKGDYQEQ 112 G++L + IA+ PE R++ L++ EN+ + G++ + ++Q Sbjct: 318 AGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIILALQARIGWWRYLSNTRQQ 377 Query: 113 ------MDKVLHLFPRLKERFTQRGGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAP 166 +DK+ P + Q +SGG QQ + + R L +P LL+LDEP+ G+ Sbjct: 378 EIAQFFIDKLQIATPDADKPIEQ----LSGGNQQKVILARWLAIEPILLVLDEPTRGIDI 433 Query: 167 IIIQQIFDIIEQLRKDGVTVFLVEQNANQALKIADRAYVLENGRVVMQGTGEALLTDPKV 226 +I +I L +G+++ + ++ + +++ VL + V + +G A LT V Sbjct: 434 GAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDRYAVRELSG-AELTSQHV 492 Query: 227 REAYLGG 233 +A G Sbjct: 493 MQAIAEG 499 Lambda K H 0.320 0.137 0.381 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: 236 Number of extensions: 8 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: 233 Length of database: 499 Length adjustment: 28 Effective length of query: 205 Effective length of database: 471 Effective search space: 96555 Effective search space used: 96555 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 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