Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate Ga0059261_0562 Ga0059261_0562 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component
Query= reanno::acidovorax_3H11:Ac3H11_2560 (259 letters) >FitnessBrowser__Korea:Ga0059261_0562 Length = 232 Score = 115 bits (289), Expect = 6e-31 Identities = 73/184 (39%), Positives = 102/184 (55%), Gaps = 11/184 (5%) Query: 21 TQALQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDHATSGRVLLDG---APVEGPGA 77 T+ L+ +D ++ V ILGPSG GKS+L+ I++GL+ A+ G V + G ++ G Sbjct: 27 TEILKGIDVDIARGSSVAILGPSGSGKSSLMAILSGLERASGGEVSVAGIAYGTLDEDGL 86 Query: 78 ER------GMVFQSYTLFPWLTIEQNIRFGLRERGMPEAQQKERAAYFIAKVGLRGFEQH 131 R G+V Q++ L P +T +N+ L G P+A RA + VGL H Sbjct: 87 ARARRGRVGIVLQAFHLLPTMTAHENVAVPLELAGAPDAFA--RAGAELDAVGLGHRLTH 144 Query: 132 FPKQLSGGMQQRTAIARALANDPKILLMDEPFGALDNQTRVLMQELLLGIWEAERKTVLF 191 +P QLSGG QQR AIARA+A P+IL DEP G LD T + +LL A T+L Sbjct: 145 YPVQLSGGEQQRVAIARAVAGRPEILFADEPTGNLDGATSGAIVDLLFDRQRAADATLLI 204 Query: 192 VTHD 195 +THD Sbjct: 205 ITHD 208 Lambda K H 0.322 0.136 0.394 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: 143 Number of extensions: 5 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: 259 Length of database: 232 Length adjustment: 24 Effective length of query: 235 Effective length of database: 208 Effective search space: 48880 Effective search space used: 48880 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 (21.9 bits) S2: 46 (22.3 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