Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate GFF2824 PS417_14415 ABC transporter ATP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_2560 (259 letters) >FitnessBrowser__WCS417:GFF2824 Length = 267 Score = 187 bits (474), Expect = 3e-52 Identities = 101/239 (42%), Positives = 142/239 (59%), Gaps = 4/239 (1%) Query: 24 LQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDHATSGRVLLDGAPVEGPGAERGMVF 83 LQ D ++ + V+ILGPSG GKS+LLR++AGL G V + G P+ GP + F Sbjct: 21 LQGFDLHLQPGEVVSILGPSGVGKSSLLRVLAGLQAPQGGSVRVLGEPLNGPHPRVAVAF 80 Query: 84 QSYTLFPWLTIEQNIRFGL---RERGMPEAQQKERAAYFIAKVGLRGFEQHFPKQLSGGM 140 Q +L PWL +E+N+ FGL R+ + +++ R + IA VGL Q FP QLSGGM Sbjct: 81 QDPSLLPWLNLEKNVAFGLDFARQPHLDHDERRRRIDHAIAAVGLEQARQQFPAQLSGGM 140 Query: 141 QQRTAIARALANDPKILLMDEPFGALDNQTRVLMQELLLGIWEAERKTVLFVTHDIDEAI 200 QRTA+AR LA P++LL+DEPFGALD TR MQ LLL + + + +THDIDEA+ Sbjct: 141 AQRTALARCLARQPQVLLLDEPFGALDEVTRADMQHLLLKVNREQGSAAVLITHDIDEAL 200 Query: 201 FMANRVAVFSARPGRIKTELAVDLPHPRHYTIKTSPEF-MDLKARLTEEIRAESMAADL 258 +++R+ + RP R E +DLP PR ++ +D+ L + R +S DL Sbjct: 201 LLSDRILLLGNRPARTLGEWLIDLPQPREEQVEAIGALRIDILKTLRQASRPQSNPLDL 259 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: 201 Number of extensions: 9 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: 267 Length adjustment: 25 Effective length of query: 234 Effective length of database: 242 Effective search space: 56628 Effective search space used: 56628 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