Align histidine transport ATP-binding protein hisP (characterized)
to candidate Synpcc7942_1305 Synpcc7942_1305 ATPase
Query= CharProtDB::CH_003210 (257 letters) >FitnessBrowser__SynE:Synpcc7942_1305 Length = 536 Score = 129 bits (324), Expect = 1e-34 Identities = 84/236 (35%), Positives = 133/236 (56%), Gaps = 17/236 (7%) Query: 23 GVSLQANAGDVISIIGSSGSGKSTFLRCINFLEKPSEGSIVVNGQTINLVRDKDGQLKVA 82 G+SL+ G+ + +IG SG GKST LR I L +PS+G ++ GQ + + D+ Sbjct: 302 GLSLEVWPGETLGLIGESGCGKSTLLRTILQLLRPSQGKVLFQGQDLTQLPDR------- 354 Query: 83 DKNQLRLLRTRLTMVFQH--FNLWSHMTVLENVMEAPIQVLGLSK-QEARERAVKYLAKV 139 +LR LR L ++FQ L +T+ + + + P+++ GL++ A+++ + L +V Sbjct: 355 ---RLRSLRRELQLIFQDPAACLNPRLTIGDAIAD-PLKIQGLARGAAAKQQVLAILEQV 410 Query: 140 GIDERAQ--GKYPVHLSGGQQQRVSIARALAMEPEVLLFDEPTSALDPELVGEVLRIMQQ 197 G+ +YP LSGGQQQRV+IARAL P+++L DEP S LD + +VL +MQ+ Sbjct: 411 GLTPAPTWIDRYPHQLSGGQQQRVAIARALITRPKLVLCDEPVSMLDATVQAQVLALMQE 470 Query: 198 LAEE-GKTMVVVTHEMGFARHVSTHVIFLHQGKIEEEGAPEQLFGNPQSPRLQRFL 252 L ++ T + VTH++ AR V L +GKI E G Q+ P+ P + L Sbjct: 471 LKQQLNLTYLFVTHDLRVAREFCDRVAVLQRGKIVEIGPAAQVLTQPEHPYTRSLL 526 Score = 107 bits (268), Expect = 4e-28 Identities = 71/244 (29%), Positives = 130/244 (53%), Gaps = 12/244 (4%) Query: 17 EHEVLKGVSLQANAGDVISIIGSSGSGKSTFLRCINFLEKPS---EGSIVVNGQTINLVR 73 E L+ +SL+ AG+ + ++G SG GKST R I L P +G I + GQ + Sbjct: 17 EQPALQQLSLELAAGERLGLVGESGCGKSTLGRAILRLLPPGSHQQGDIRLAGQAL---- 72 Query: 74 DKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEA-PIQVLGLSKQEARERA 132 GQL+ + R + L L T+ ++++E + LS+++A+++A Sbjct: 73 ---GQLQGRSLQRFRGGQVGLVFQDPMTRLDPLQTIGDHLLETLQVHRPHLSRRQAKQQA 129 Query: 133 VKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPEVLLFDEPTSALDPELVGEVL 192 + +L +V I +YP SGG +QRV+IA AL ++P +++ DEPT++LD + E+L Sbjct: 130 LSWLERVRIPANRWSQYPHQFSGGMRQRVAIALALLLQPRLVVADEPTTSLDVTVAAEIL 189 Query: 193 RIMQQL-AEEGKTMVVVTHEMGFARHVSTHVIFLHQGKIEEEGAPEQLFGNPQSPRLQRF 251 + + +L +EE ++++++H++ + L+QG++ E G + PQ P Q Sbjct: 190 QELTRLCSEENTSLLLISHDLPMVAAYCDRIAVLYQGQLVETGPTTAVLTRPQHPYTQTL 249 Query: 252 LKGS 255 L+ + Sbjct: 250 LQSA 253 Lambda K H 0.318 0.134 0.375 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: 305 Number of extensions: 16 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 257 Length of database: 536 Length adjustment: 30 Effective length of query: 227 Effective length of database: 506 Effective search space: 114862 Effective search space used: 114862 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 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