Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate WP_011382978.1 AMB_RS02755 nitrate/sulfonate/bicarbonate ABC transporter ATP-binding protein
Query= reanno::psRCH2:GFF857 (371 letters) >NCBI__GCF_000009985.1:WP_011382978.1 Length = 553 Score = 162 bits (409), Expect = 3e-44 Identities = 101/248 (40%), Positives = 146/248 (58%), Gaps = 8/248 (3%) Query: 1 MASVTLRDICKSYDGTPITRHIDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDITSGDL 60 M + L+ + KSY + + R IDL+IEDGEF+ +G SG GK+TL+ L+AGL +G++ Sbjct: 1 MPILELKGVAKSYGASSVLRDIDLEIEDGEFIAILGFSGSGKTTLVSLMAGLIKPDAGEV 60 Query: 61 LIDNQRVNDLPPKDRSVGMVFQSYALYPHMTVAENMAFGLKLASVD--KREIKRRVEAVA 118 L+ + V D P DR G+VFQSY+L P +TV N+A + D K E K RV Sbjct: 61 LLRGKPV-DGPGADR--GVVFQSYSLMPWLTVEGNIALAVDAVMPDASKAERKARVAKYI 117 Query: 119 EILQLDKLLERKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAFLRVQMRIEIAR 178 ++ L ER+P +LSGG RQRVA+ R + P + L DEPLS LDA R +++ EI Sbjct: 118 GMVGLSHAAERRPSELSGGMRQRVAVARALAMSPDILLLDEPLSALDALTRAKLQDEIEA 177 Query: 179 LHQRIRSTMIYVTHDQVEAMTLADKIVVLNAGEIAQVGQPLHLYHYPKNRFVAGFLGSPQ 238 + ++ + T+I +T+D EA+ LAD+I+ LN G A G P + P+ R A P Sbjct: 178 IWEQEKKTVILITNDVDEALLLADRIIPLNPGPGATFG-PSFKVNLPRPRDRAAVNSDP- 235 Query: 239 MNFVEVRA 246 +F +RA Sbjct: 236 -DFKRLRA 242 Score = 136 bits (342), Expect = 2e-36 Identities = 83/226 (36%), Positives = 129/226 (57%), Gaps = 8/226 (3%) Query: 23 DLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDITSGDLLIDNQRVNDLPPKDRSVGMVFQ 82 DL + GEF+ +G SGCGKST+L + AGL D++ G +++D + V++ P DR+V VFQ Sbjct: 316 DLKMHQGEFISLIGHSGCGKSTVLTMTAGLTDVSEGGVILDGREVSEAGP-DRAV--VFQ 372 Query: 83 SYALYPHMTVAENMAFGLKLASVDKREIKRR--VEAVAEILQLDKLLERKPKDLSGGQRQ 140 + +L+P +T +N+A G+ +R V E + L +++K D+S G RQ Sbjct: 373 APSLFPWLTALQNVALGVDRVYPHASPAERLDIVSYYLERVGLGDSMDKKASDMSNGMRQ 432 Query: 141 RVAIGRTMVREPKVFLFDEPLSNLDAFLRVQMRIEIARLHQRIRSTMIYVTHDQVEAMTL 200 RV I R PK+ L DEP LD+ R +++ + + R R T I VTHD EA+ L Sbjct: 433 RVGIARAFALSPKLLLLDEPFGMLDSLTRWELQEVLMEVWTRTRVTAICVTHDVDEAILL 492 Query: 201 ADKIVVLNAGEIAQVGQPLHLYHYPKNRFVAGFLGSPQMNFVEVRA 246 ADK+V++ G A++G+ L++ P+ R L P+ + E RA Sbjct: 493 ADKVVMMTNGPNARIGKVLNV-DIPRPRTRRALLEHPR--YYEYRA 535 Lambda K H 0.322 0.139 0.405 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: 499 Number of extensions: 32 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: 371 Length of database: 553 Length adjustment: 33 Effective length of query: 338 Effective length of database: 520 Effective search space: 175760 Effective search space used: 175760 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: 51 (24.3 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