Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate WP_086508158.1 BZY95_RS01100 maltose ABC transporter permease MalF
Query= reanno::psRCH2:GFF850 (521 letters) >NCBI__GCF_002151265.1:WP_086508158.1 Length = 537 Score = 554 bits (1427), Expect = e-162 Identities = 297/531 (55%), Positives = 368/531 (69%), Gaps = 37/531 (6%) Query: 14 RPTSWGLPRFLTTGVRWLLWLAFNALSLYLVVALYVQKQMAFALLGLVVTGIASYLFINR 73 R T W L + V LLWL V+A ++ Q FALL LV+ +F R Sbjct: 21 RYTRWALRSLVAALVLALLWL---------VLAFHLNGQPIFALLFLVLGAALGVVFTRR 71 Query: 74 RMYAQRYIFPSVAGMLVFVIFPLLYTVGIGFTNYSGTNLLSQAQVERYHLSQTYLA-GER 132 + + RYIFP+VA M +FVIFPLLYTVGI F+NYS +NLLS+ +V LS+TY Sbjct: 72 TLMSHRYIFPAVASMALFVIFPLLYTVGISFSNYSSSNLLSEERVRAQLLSRTYQEESTT 131 Query: 133 FRFTLHQSPDGERLRVDKGELGVFVSPPLTGEPDPE-------------APLSLLPAE-- 177 F F L+ S +G RL +++ +PP TGE + E PLSL E Sbjct: 132 FGFQLYSSDEGVRLYLEREG-----APPTTGEAEAELEEALEGVSRFVTGPLSLQDGERR 186 Query: 178 -------SVEGLGEALALREVIQRRKVLEQWVMQAPDGSLLRLYGLREVAAVEPQYRQDG 230 + E +GE L +REV+ R L+ V+ P+G LR+ GLR A + +Y Sbjct: 187 HVAIQPAAGEPVGEPLPMREVVAYRTALQNLVLATPEGLELRMAGLRHYAPMLDRYEVRA 246 Query: 231 PGVLVETRTGARLTADMERGFYVDETGKAVPPGFTVFTGFANFSRVLTEPSIREPFMQIF 290 G L + R LTAD E GF+V E G+ + PG+ V G N++R+ +P IR PF+QIF Sbjct: 247 DGSLYDRRDDLLLTADGETGFFVTEEGERITPGWPVAVGLDNYARIFLDPDIRGPFIQIF 306 Query: 291 AWTFAFAGLTVVFTLAVGLVLASLLQWELVRGKAFYRLMLILPYAVPGFISILVFRGLFN 350 WTFAFAGLTV+FTL VG VLASLLQW+ +RGKA YR +LILPYAVP FISIL+F+G+FN Sbjct: 307 VWTFAFAGLTVLFTLIVGFVLASLLQWDQLRGKALYRTLLILPYAVPAFISILIFKGMFN 366 Query: 351 QNFGEINLLLEGLFGIRPDWFSDPSLARTMILIVNTWLGYPYMLLLCMGLLQAIPRDQYE 410 Q+FGEINL+L+ LFG+RPDWF+DP LAR+M+LIVNTWLGYPYMLLLCMGL+Q+IPRD YE Sbjct: 367 QHFGEINLILDALFGVRPDWFTDPWLARSMLLIVNTWLGYPYMLLLCMGLIQSIPRDLYE 426 Query: 411 ASAIDGASPLDNLLRITLPQLIKPLMPLLIACFAFNFNNFVLITLLTRGGPDIIGATTPA 470 ASA+DG PL NL +ITLP +IKPL PLLIACFAFNFNNFVLI LLT G PDI+GA+TPA Sbjct: 427 ASAVDGGGPLTNLFQITLPLIIKPLTPLLIACFAFNFNNFVLIALLTGGNPDILGASTPA 486 Query: 471 GTTDLLVSYTYRIAFQDSGQDFALAAAIATMIFILVGAMALLNLKLSKVKV 521 GTTDLLVSYTYRIAFQD+GQ+F LAAAIAT+IF+LV +ALLNL+L+KV+V Sbjct: 487 GTTDLLVSYTYRIAFQDAGQNFGLAAAIATLIFLLVAGLALLNLRLAKVRV 537 Lambda K H 0.327 0.142 0.429 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: 894 Number of extensions: 47 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: 521 Length of database: 537 Length adjustment: 35 Effective length of query: 486 Effective length of database: 502 Effective search space: 243972 Effective search space used: 243972 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 24 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