Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate 8500413 DvMF_1163 ABC transporter related (RefSeq)
Query= uniprot:Q1MCU2 (292 letters) >FitnessBrowser__Miya:8500413 Length = 255 Score = 202 bits (514), Expect = 6e-57 Identities = 114/259 (44%), Positives = 165/259 (63%), Gaps = 11/259 (4%) Query: 14 LLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMITF 73 LL+++ ++ +FGGL A++DF+ + + ALIGPNGAGKTTVFN ++GFY+PT G I F Sbjct: 3 LLEMKGVTQRFGGLQAVSDFNISLEERKLIALIGPNGAGKTTVFNLVSGFYQPTEGQIIF 62 Query: 74 NQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKLMKASGYTIL 133 + K L ++T +ARTFQNIRL+ ++VL+N+ +AQH++L GYTI Sbjct: 63 DGKP-----TAGLRPHQVTARG-IARTFQNIRLWHEMSVLDNIRIAQHHRL----GYTIW 112 Query: 134 -GLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCTGPEL 192 + G + R +A LE DL D A + +LPYG QRR+EIARAM P+L Sbjct: 113 DAFLRTGRFTRSEGNIDTIAWEMLEAMDLKDAAHELPRNLPYGLQRRVEIARAMSIRPKL 172 Query: 193 LCLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYGQKIS 252 L LDEPAAGLN + L L++ I E +I +IEH M VVM + + + V+++G I+ Sbjct: 173 LLLDEPAAGLNSADVDGLIKLIRWIHDEFDIAIWMIEHQMKVVMSLCEWIKVIDFGSTIA 232 Query: 253 DGTPDHVKNDPRVIAAYLG 271 +GTP+ ++++P VI AYLG Sbjct: 233 EGTPEEIQSNPVVIKAYLG 251 Lambda K H 0.318 0.136 0.386 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: 197 Number of extensions: 9 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 292 Length of database: 255 Length adjustment: 25 Effective length of query: 267 Effective length of database: 230 Effective search space: 61410 Effective search space used: 61410 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 (21.7 bits) S2: 47 (22.7 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