Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate 3607108 Dshi_0530 ABC transporter related (RefSeq)
Query= uniprot:B2T9V9 (510 letters) >FitnessBrowser__Dino:3607108 Length = 498 Score = 273 bits (699), Expect = 8e-78 Identities = 183/505 (36%), Positives = 269/505 (53%), Gaps = 33/505 (6%) Query: 15 VEALEVTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVRFS 74 ++ +TKR+ AL+ V V PGE+ L G NG+GKSTL+ I++G+ G V+ + Sbjct: 10 IDLRAITKRYAGVTALDSVDFTVQPGEAVCLAGENGSGKSTLIKIISGVEPATAGTVQIA 69 Query: 75 GAAAPSIADRDAWRERVACVYQHSTIIRDLSVAENL-FINRQPLRGGVIDWQAMRRDARA 133 G ++ R + V ++Q ++ +LSVAEN+ F + R + ++A+R ARA Sbjct: 70 GQEHVTLNPRISAAAGVMVIFQDFSLFPNLSVAENIAFTTQLSTRQRLFKFRAVRDIARA 129 Query: 134 LLDHWKIDVREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRLFRRI 193 LD + + DAR L V +QLV I RAL+ A+ II+DEPT L E++RL I Sbjct: 130 ALDRIGVQIDLDARVETLPVAQKQLVAICRALASKAQLIIMDEPTTALTEKEVRRLQGII 189 Query: 194 SELQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAMTGERGGL 253 L+ EGV +F+SH L EV E+ + V VLR+ + + P S + L MTG Sbjct: 190 RMLKEEGVAVIFVSHKLAEVLEVSEKVVVLRNGKKVAEGPASEFDTQSLTYHMTGRDVPE 249 Query: 254 AVADAAARGALPADTAVALELKELTGA-DYEGVSFTVKRGEVVGLTGATSSGRTSVAEAI 312 A GA ++++ L A + +SF ++ GEV+G+TG GRTSVA+A+ Sbjct: 250 VPPSDVAAGA-----QTLMQVQGLGKAGSFSDISFDLRTGEVLGITGLLGCGRTSVAKAL 304 Query: 313 AGLRAAKRGTISVDGAILPPGDVPASLAHGIGCVPKDRHHEGLVLTQSVAENASM----- 367 GL G+I VDG+ +P GD A+ IG VP+DR EGL L+QS+ N ++ Sbjct: 305 FGLVTPDAGSILVDGSPVPLGDPQAASLARIGYVPEDRLTEGLFLSQSILRNVAVGRLDA 364 Query: 368 -TIARVLGKFGIAAPAKKNAFGQKMIDALGIVAQGPEHVVSGLSGGNQQKVVMARALATN 426 T L G+A A + L + A E V LSGGNQQ+V +AR L+ Sbjct: 365 HTSGGFLDMTGLAKEA------SDWLRRLKVKAPDVEAPVQSLSGGNQQRVALARWLSRA 418 Query: 427 PNVLVLIDPTAGVDVKSKEALLSVVDRVREEGKAVLVVSGELDD-LRTCDRVLVMFRGRV 485 P VL+L P+ GVDV SK + ++ + EG V+V+S +L + L TC RVLVM GR+ Sbjct: 419 PRVLILNGPSVGVDVGSKADIHDIIRELAREGIGVIVISDDLPELLATCHRVLVMREGRI 478 Query: 486 AAEFPAGWQDHDLIASVEGVSLHEE 510 I ++EG +L E+ Sbjct: 479 -------------IDALEGTALTED 490 Score = 78.6 bits (192), Expect = 5e-19 Identities = 62/233 (26%), Positives = 104/233 (44%), Gaps = 6/233 (2%) Query: 16 EALEVTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVRFSG 75 + L + G + +D+S + GE + G G G++++ L GL PD G + G Sbjct: 260 QTLMQVQGLGKAGSFSDISFDLRTGEVLGITGLLGCGRTSVAKALFGLVTPDAGSILVDG 319 Query: 76 AAAPSIADRDAWRERVACVYQHST---IIRDLSVAENLFINRQPLR--GGVIDWQAMRRD 130 + P + A R+ V + + S+ N+ + R GG +D + ++ Sbjct: 320 SPVPLGDPQAASLARIGYVPEDRLTEGLFLSQSILRNVAVGRLDAHTSGGFLDMTGLAKE 379 Query: 131 ARALLDHWKIDVRE-DARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRL 189 A L K+ + +A LS +Q V +AR LS R +IL+ P+ +D + Sbjct: 380 ASDWLRRLKVKAPDVEAPVQSLSGGNQQRVALARWLSRAPRVLILNGPSVGVDVGSKADI 439 Query: 190 FRRISELQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQL 242 I EL REG+ + IS L E+ C V V+R+ R I + +AL + L Sbjct: 440 HDIIRELAREGIGVIVISDDLPELLATCHRVLVMREGRIIDALEGTALTEDDL 492 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: 591 Number of extensions: 27 Number of successful extensions: 9 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: 510 Length of database: 498 Length adjustment: 34 Effective length of query: 476 Effective length of database: 464 Effective search space: 220864 Effective search space used: 220864 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: 52 (24.6 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