Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate 6936480 Sama_0668 iron(III) ABC transporter, ATP-binding protein (RefSeq)
Query= reanno::acidovorax_3H11:Ac3H11_2560 (259 letters) >FitnessBrowser__SB2B:6936480 Length = 341 Score = 147 bits (371), Expect = 3e-40 Identities = 86/223 (38%), Positives = 130/223 (58%), Gaps = 16/223 (7%) Query: 1 MSSVSIQAVSRVFETAKGQRTQALQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDHA 60 MS++SIQ + + +G+ Q L+ ++ + + +LGPSGCGK+TLLR +AGL Sbjct: 1 MSTLSIQGLHSDY---RGE--QVLRGLNLTLTQGEITALLGPSGCGKTTLLRTIAGLQDI 55 Query: 61 TSGRVLLDGAPVEGPGA-------ERGMVFQSYTLFPWLTIEQNIRFGLRERGMPEAQQK 113 ++G + ++G V G GM+FQ Y LFP LT+ NI FG+R+ + + + Sbjct: 56 SAGSIAINGKTVSADGCFVAPEKRSIGMIFQDYALFPHLTVADNILFGVRQ--LDKQSRS 113 Query: 114 ERAAYFIAKVGLRGFEQHFPKQLSGGMQQRTAIARALANDPKILLMDEPFGALDNQTRVL 173 R ++ V L G + +P +LSGG QQR +IARALA +P +LL+DEPF +D Q R Sbjct: 114 VRLEEMLSLVKLEGLGKRYPHELSGGQQQRVSIARALAYEPDLLLLDEPFSNIDAQVRRA 173 Query: 174 MQELLLGIWEAERKTVLFVTHDIDEAIFMANRVAVFSARPGRI 216 + + I +A + +FVTH DEA A+ +A+F A GRI Sbjct: 174 LMLEIRAILKARNVSAVFVTHSKDEAFAFADTLALFEA--GRI 214 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: 199 Number of extensions: 6 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: 341 Length adjustment: 26 Effective length of query: 233 Effective length of database: 315 Effective search space: 73395 Effective search space used: 73395 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: 48 (23.1 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