Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate CCNA_03235 CCNA_03235 spermidine/putrescine transport ATP-binding protein potA
Query= reanno::acidovorax_3H11:Ac3H11_2560 (259 letters) >FitnessBrowser__Caulo:CCNA_03235 Length = 381 Score = 156 bits (395), Expect = 5e-43 Identities = 85/199 (42%), Positives = 123/199 (61%), Gaps = 3/199 (1%) Query: 15 TAKGQRTQALQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDHATSGRVLLDGAPVEG 74 T + + A+ V V + +F +LGPSGCGK+TLLR++AG + T GR+L+DG + Sbjct: 21 TKRFGKLAAVDNVSLTVNEGEFFALLGPSGCGKTTLLRMLAGFETPTEGRILIDGQDISN 80 Query: 75 -PGAER--GMVFQSYTLFPWLTIEQNIRFGLRERGMPEAQQKERAAYFIAKVGLRGFEQH 131 P +R MVFQSY +FP +T+ N+ +GL+ +P+A+++ R A + V L G Sbjct: 81 VPPNKRPVNMVFQSYAVFPHMTVADNVAYGLKVDNVPKAEREARVAEALELVQLGGLGGR 140 Query: 132 FPKQLSGGMQQRTAIARALANDPKILLMDEPFGALDNQTRVLMQELLLGIWEAERKTVLF 191 P QLSGG +QR A+ARAL P++LL+DEP ALD + R M+ L + E T + Sbjct: 141 KPDQLSGGQRQRVALARALVKRPRVLLLDEPLSALDAKLREQMRTELCTLQEKVGITFIM 200 Query: 192 VTHDIDEAIFMANRVAVFS 210 VTHD DEA+ +A+R AV S Sbjct: 201 VTHDQDEALALASRCAVMS 219 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: 229 Number of extensions: 12 Number of successful extensions: 2 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: 381 Length adjustment: 27 Effective length of query: 232 Effective length of database: 354 Effective search space: 82128 Effective search space used: 82128 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