Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate GFF3902 HP15_3842 iron(III) ABC transporter, ATP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_2560 (259 letters) >FitnessBrowser__Marino:GFF3902 Length = 371 Score = 148 bits (373), Expect = 2e-40 Identities = 81/201 (40%), Positives = 121/201 (60%), Gaps = 12/201 (5%) Query: 24 LQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDHATSGRVLLDGAPVEGPGAER---- 79 ++ ++ + + V +LGPSGCGK+TLLRI AGL T G+V L + V PG + Sbjct: 38 VKDINLHLEAGEVVCLLGPSGCGKTTLLRIAAGLQMPTRGKVFLGSSLVSAPGGVQVPPE 97 Query: 80 ----GMVFQSYTLFPWLTIEQNIRFGLRERGMPEAQQKERAAYFIAKVGLRGFEQHFPKQ 135 G+ FQ LFP LT+ +N+ FG+ MP+ QQ+ RA + ++G+ +P Sbjct: 98 KRNVGLAFQESALFPHLTVLENVCFGISS--MPKKQQRTRALELLGRLGMADAANVYPHT 155 Query: 136 LSGGMQQRTAIARALANDPKILLMDEPFGALDNQTRVLMQELLLGIWEAERKTVLFVTHD 195 LSGG QQR A+ARALA P+++L+DEPF +LD + R +++ L + + L VTHD Sbjct: 156 LSGGQQQRVALARALAPSPRVMLLDEPFSSLDARLRDQIRDDTLHVLKELNTATLLVTHD 215 Query: 196 IDEAIFMANRVAVFSARPGRI 216 +EA+FMA+R+A+ R G I Sbjct: 216 PEEAMFMADRIALM--RDGEI 234 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: 236 Number of extensions: 10 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: 371 Length adjustment: 27 Effective length of query: 232 Effective length of database: 344 Effective search space: 79808 Effective search space used: 79808 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