Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate WP_012591930.1 MSIL_RS15015 ribosome-associated ATPase/putative transporter RbbA
Query= uniprot:B2T9V9 (510 letters) >NCBI__GCF_000021745.1:WP_012591930.1 Length = 943 Score = 122 bits (305), Expect = 8e-32 Identities = 129/504 (25%), Positives = 219/504 (43%), Gaps = 57/504 (11%) Query: 14 VVEALEVTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVRF 73 V E V+ R+G+ AL+DV+I + G L+G +G GKS+L+S++ G R+ +G+V Sbjct: 8 VGELYGVSLRYGARVALDDVTISLPAGRMVGLIGPDGVGKSSLLSLIAGARRIQSGQVHV 67 Query: 74 SGAAAPSIADRDAWRERVACVYQ--HSTIIRDLSVAENLFINRQPLRGGVIDWQAMRRDA 131 G R ++A + Q + DLSV EN+ G + RD Sbjct: 68 LGGDLGDPRHRADVCPQIAYMPQGLGKNLYPDLSVRENI-----EFFGRLFGQSKDERDR 122 Query: 132 R--ALLDHWKIDVREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRL 189 R ALL +D D A LS RQ + + AL + +ILDEPT +D ++ Sbjct: 123 RIAALLTATGLDPFPDRPASKLSGGMRQKLGLCCALIHDPDLLILDEPTTGVDPLSRRQF 182 Query: 190 FRRISEL--QREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSA---------PVSALP 238 + IS + +R G++ + + +++E + V + DA I++A S+ Sbjct: 183 WSLISRMRAERRGMSVIVATAYMEEADQFHWLVAM--DAGRILAAGSPSDLKAKTNSSSL 240 Query: 239 REQLIEAMTGERGGLAVADAAARGALPADTAVALELKELTG-----ADYEGVSFTVKRGE 293 E I + ER A D + ++LT + VSF++KRGE Sbjct: 241 EESFIALLPEERRRGHKAFTIGPRPPGDDGEPVIVARDLTRRFGEFVAVDRVSFSIKRGE 300 Query: 294 VVGLTGATSSGRTSVAEAIAGLRAAKRGTISVDGAILPPGDVPASLAHGIGCVPKDRHHE 353 + G G+ G+++ + + GL A G + G + D+ A G + E Sbjct: 301 IFGFLGSNGCGKSTTMKMLTGLLPASAGEAFLFGEAVDASDMKARFRVGYMSQSFSLYSE 360 Query: 354 GLV---------LTQSVAENASMTIARVLGKFGIAAPAKKNAFGQKMIDALGIVAQGPEH 404 V L E A IA + +FG+ ++ Q+ D Sbjct: 361 LTVRQNLDLHAHLFHIAREKARARIADLTARFGL-----EDFLDQRTAD----------- 404 Query: 405 VVSGLSGGNQQKVVMARALATNPNVLVLIDPTAGVDVKSKEALLSVV-DRVREEGKAVLV 463 L G +Q++ +A A+ P +L+L +PT+GVD +++ ++ D R EG + + Sbjct: 405 ----LPLGIRQRLSLAVAIVHEPEILILDEPTSGVDPLARDRFWDLLADLSRGEGVTIFI 460 Query: 464 VSGELDDLRTCDRVLVMFRGRVAA 487 + +++ CDR+ +M GRV A Sbjct: 461 STHFMNEAARCDRIALMDAGRVLA 484 Score = 91.7 bits (226), Expect = 1e-22 Identities = 78/262 (29%), Positives = 122/262 (46%), Gaps = 11/262 (4%) Query: 13 PVVEALEVTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVR 72 PV+ A ++T+RFG A++ VS + GE +G NG GKST + +LTGL GE Sbjct: 272 PVIVARDLTRRFGEFVAVDRVSFSIKRGEIFGFLGSNGCGKSTTMKMLTGLLPASAGEAF 331 Query: 73 FSGAAAPSIADRDAWRERVACVYQHSTIIRDLSVAENLFINRQPLRGGVIDWQAMRRDAR 132 G A + +D A R RV + Q ++ +L+V +NL ++ I + R Sbjct: 332 LFGEAVDA-SDMKA-RFRVGYMSQSFSLYSELTVRQNLDLHAHLFH---IAREKARARIA 386 Query: 133 ALLDHWKIDVREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRLFRR 192 L + ++ D R DL + RQ + +A A+ + +ILDEPT+ +D R + Sbjct: 387 DLTARFGLEDFLDQRTADLPLGIRQRLSLAVAIVHEPEILILDEPTSGVDPLARDRFWDL 446 Query: 193 ISELQR-EGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAP----VSALPREQLIEAMT 247 +++L R EGVT +FIS H C + ++ R + + V A R L +A Sbjct: 447 LADLSRGEGVT-IFISTHFMNEAARCDRIALMDAGRVLATGTPAELVKARQRTNLEDAFI 505 Query: 248 GERGGLAVADAAARGALPADTA 269 A+A G P A Sbjct: 506 DYLEEANAAEARRSGPRPETAA 527 Score = 71.6 bits (174), Expect = 1e-16 Identities = 66/229 (28%), Positives = 111/229 (48%), Gaps = 13/229 (5%) Query: 283 EGVSFTVKRGEVVGLTGATSSGRTSVAEAIAGLRAAKRGTISVDGAILPPGDVPASLAHG 342 + V+ ++ G +VGL G G++S+ IAG R + G + V G L A + Sbjct: 25 DDVTISLPAGRMVGLIGPDGVGKSSLLSLIAGARRIQSGQVHVLGGDLGDPRHRADVCPQ 84 Query: 343 IGCVPKDRHHEGLVLTQSVAENASMTIARVLGKFGIAAPAKKNAFGQKMIDALGIVAQGP 402 I +P+ + L SV EN R+ G+ + +++ ++ A G+ P Sbjct: 85 IAYMPQGLG-KNLYPDLSVRENIEF-FGRLFGQ----SKDERDRRIAALLTATGL-DPFP 137 Query: 403 EHVVSGLSGGNQQKVVMARALATNPNVLVLIDPTAGVDVKSKEALLSVVDRVREE--GKA 460 + S LSGG +QK+ + AL +P++L+L +PT GVD S+ S++ R+R E G + Sbjct: 138 DRPASKLSGGMRQKLGLCCALIHDPDLLILDEPTTGVDPLSRRQFWSLISRMRAERRGMS 197 Query: 461 VLVVSGELDDLRTCDRVLVMFRGRVAAEFPAGWQDHDLIASVEGVSLHE 509 V+V + +++ ++ M GR+ A AG DL A SL E Sbjct: 198 VIVATAYMEEADQFHWLVAMDAGRILA---AG-SPSDLKAKTNSSSLEE 242 Lambda K H 0.318 0.134 0.377 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: 950 Number of extensions: 46 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 510 Length of database: 943 Length adjustment: 39 Effective length of query: 471 Effective length of database: 904 Effective search space: 425784 Effective search space used: 425784 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: 54 (25.4 bits)
This GapMind analysis is from Apr 09 2024. 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