Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate HSERO_RS01865 HSERO_RS01865 sulfonate ABC transporter ATP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_2560 (259 letters) >FitnessBrowser__HerbieS:HSERO_RS01865 Length = 269 Score = 238 bits (606), Expect = 1e-67 Identities = 122/249 (48%), Positives = 165/249 (66%), Gaps = 4/249 (1%) Query: 4 VSIQAVSRVFETAKGQRTQALQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDHATSG 63 + IQ V +VF+T + AL+ ++ ++ D FV +LGPSGCGKSTLL +AG +SG Sbjct: 10 IRIQGVHKVFKT-DDREVVALKDINLDIPDGQFVCLLGPSGCGKSTLLNAIAGFALPSSG 68 Query: 64 RVLLDGAPVEGPGAERGMVFQSYTLFPWLTIEQNIRFGLRERGMPEAQQKERAAYFIAKV 123 ++L D V PG +RGMVFQ Y LFPW+T+EQN+ FGL +G P+A+ +R + K+ Sbjct: 69 QILTDDKVVSEPGPDRGMVFQEYALFPWMTVEQNVAFGLEIKGTPKAEIHQRVTQLLDKL 128 Query: 124 GLRGFEQHFPKQLSGGMQQRTAIARALANDPKILLMDEPFGALDNQTRVLMQELLLGIWE 183 GL F FPK LSGGM+QR AIAR LA D I+LMDEPFGALD TR +Q+ LL IW+ Sbjct: 129 GLIDFRTRFPKDLSGGMRQRVAIARVLALDSPIMLMDEPFGALDALTRRNLQDELLRIWD 188 Query: 184 AERKTVLFVTHDIDEAIFMANRVAVFSARPGRIKTELAVDLPHPRHYTIKTSPEFMDLKA 243 RKT++FVTH I+EAI++A+R+ V + RPG +K ++ V+LP R PEF LK Sbjct: 189 EFRKTIVFVTHSIEEAIYLADRIVVMTYRPGTVKRDMLVNLPRLRD---PADPEFNALKR 245 Query: 244 RLTEEIRAE 252 L + + E Sbjct: 246 ELGQLVMEE 254 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: 202 Number of extensions: 4 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: 269 Length adjustment: 25 Effective length of query: 234 Effective length of database: 244 Effective search space: 57096 Effective search space used: 57096 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