Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate PfGW456L13_2816 Various polyols ABC transporter, ATP-binding component
Query= reanno::acidovorax_3H11:Ac3H11_2560 (259 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2816 Length = 282 Score = 248 bits (633), Expect = 1e-70 Identities = 126/231 (54%), Positives = 160/231 (69%) Query: 22 QALQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDHATSGRVLLDGAPVEGPGAERGM 81 +A+Q +D ++ FV ILGPSGCGKSTLL +AG +G + +DGA V GP +RGM Sbjct: 28 EAVQGLDCQIEPGQFVCILGPSGCGKSTLLGALAGHLQPRTGTLNVDGAAVSGPSPQRGM 87 Query: 82 VFQSYTLFPWLTIEQNIRFGLRERGMPEAQQKERAAYFIAKVGLRGFEQHFPKQLSGGMQ 141 VFQ +TLFPW T+ N+ FGL+ RG+ +A++ + A +A VGL GF +P QLSGGMQ Sbjct: 88 VFQQHTLFPWRTVRDNVAFGLKMRGVGKAERHKAADEILALVGLEGFAGRWPDQLSGGMQ 147 Query: 142 QRTAIARALANDPKILLMDEPFGALDNQTRVLMQELLLGIWEAERKTVLFVTHDIDEAIF 201 QR IAR L N P++LLMDEPFGALD TR+ MQELLL IW R TV+FVTHDIDEA+F Sbjct: 148 QRVEIARVLVNRPRLLLMDEPFGALDALTRLNMQELLLDIWTRIRTTVVFVTHDIDEALF 207 Query: 202 MANRVAVFSARPGRIKTELAVDLPHPRHYTIKTSPEFMDLKARLTEEIRAE 252 +A+R+ V S+RPGRI +L +D P PR + T PEF LK E +R E Sbjct: 208 LADRLLVMSSRPGRIIEDLRLDFPRPRSTELMTRPEFSHLKRHCLELLRHE 258 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: 239 Number of extensions: 8 Number of successful extensions: 1 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: 282 Length adjustment: 25 Effective length of query: 234 Effective length of database: 257 Effective search space: 60138 Effective search space used: 60138 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: 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