Align Solute-binding (Aliphatic amino acid) component of ABC transporter (characterized, see rationale)
to candidate WP_012043137.1 BBTA_RS13980 amino acid ABC transporter
Query= uniprot:Q1MDE9 (367 letters) >NCBI__GCF_000015165.1:WP_012043137.1 Length = 386 Score = 83.2 bits (204), Expect = 1e-20 Identities = 105/350 (30%), Positives = 151/350 (43%), Gaps = 37/350 (10%) Query: 1 MTLKTLTATLVASLAFAPLAHA----DITIGLIAPLTGPVAAYGDQVKNGAQTAVDEINK 56 MT + LT +L +LA L+ A I IG+ L+G + V A+ AV+EIN Sbjct: 1 MTSRLLTTSLALALAATTLSPALAVDPIKIGVPVGLSGANSVVAPSVVQSAELAVEEINA 60 Query: 57 KGGILGEKVVLELADDAGEPKQGVSAANKVVGDGIRFVVGPVTSGVAIPVSDVLAENGVL 116 KGG+LG K+ LE+ADDA G + A K D + F V I + A N L Sbjct: 61 KGGVLGRKLELEVADDA----SGAAGAQKAF-DALIF---QKKVNVLISMETSAARNAGL 112 Query: 117 MVTPTATAPDL------TKRGLTNVLRTCGRDDQQAEVAAKYVLKNFKDKRVAIVNDKGA 170 + P + K + DQQ Y K K K ++ A Sbjct: 113 PIVARGKTPYIYTSFYEGKSCSPYLYVNAWVPDQQVPPIVDYFNKEKKAKSYFLIGSDYA 172 Query: 171 YGKGLADAFKATLNAGGITEVVNDAITPGD-KDFSALTTRIKSEKVD--VVYFGGYHPEG 227 +G+G+ K + G +VV + P D D++++ +++K+ D + G P Sbjct: 173 FGRGMLGFTKTYIEKTG-GKVVGEEYLPMDGSDWTSIISKLKASGADALITSTAGGAP-N 230 Query: 228 GLLARQLHDLAANATI-IGGDGLSNTEFWAIGTDAAGGTIFTNASDAT--KSPDSKAAAD 284 L +QL AA T+ G + +G DAAG I+ +AS T +P +K Sbjct: 231 VTLTKQLR--AAGVTLPYGNLAVDEGTAKGMGADAAG--IYLSASYVTGIDTPANKTFL- 285 Query: 285 ALAAKNIPAEAFTLN-----AYAAVEVLKAGIEKAGSAEDAEAVATALKD 329 A AK AE T N Y AV KA +EKAGS D + V AL + Sbjct: 286 ASMAKKFGAELKTPNDLSVPQYEAVYAYKAAVEKAGST-DQDKVLKALAE 334 Lambda K H 0.312 0.131 0.362 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: 324 Number of extensions: 17 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 367 Length of database: 386 Length adjustment: 30 Effective length of query: 337 Effective length of database: 356 Effective search space: 119972 Effective search space used: 119972 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 50 (23.9 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