Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate WP_068005521.1 PsAD2_RS10155 ABC transporter ATP-binding protein
Query= uniprot:A0A0C4Y5F6 (540 letters) >NCBI__GCF_001623255.1:WP_068005521.1 Length = 515 Score = 271 bits (693), Expect = 4e-77 Identities = 181/523 (34%), Positives = 281/523 (53%), Gaps = 22/523 (4%) Query: 4 MSDTSTKAPLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAY 63 M +T T PLL+L+NI K F + A V L +AGE+ AL+GENGAGK+TLM IL G Y Sbjct: 1 MPETETVHPLLSLQNITKIFGDLVANGNVNLDLHAGEIVALLGENGAGKTTLMNILFGHY 60 Query: 64 TADPGGECHIDGQRVQID----GPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRR 119 AD G +D PQ+A + G+ +++Q +LA NL+ ENI LG Sbjct: 61 VADEGRVMVRTSSGTLVDLEPGAPQAALEAGIGMVHQHFTLAENLTGLENIVLGTESLFA 120 Query: 120 GLVARGDMVRACAPTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTT 179 +R + G + V+ L++ +RQ VEI +A++ +ARILV+DEPT Sbjct: 121 RKFSRSKARAKLQELMQSSGLEVDLDLRVSKLAVGERQRVEILKALYRDARILVLDEPTA 180 Query: 180 PLSTHETDRLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQ 239 L+ E+D LF ++ L +GMAI++ISH+MAE+ +DRV VLR G V L + + Sbjct: 181 VLTPQESDSLFNTLKLLAAKGMAIIFISHKMAEVLGASDRVAVLRGGRIVADLPTSQCDR 240 Query: 240 AALVKMMVGRDLSGFYTKTHGQAVEREVMLSVRDVADGRR-VKGCSFDLRAGEVLGLAGL 298 L ++MVG + + G E ++ +GR ++ + LR GE++GLAG+ Sbjct: 241 HKLAELMVGHAVQ-MAEREPGNPGEEILVFKGVSAGEGRELIENVNLSLRKGEIIGLAGV 299 Query: 299 VGAGRTELARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQ 358 G G++ LA+++ G + T G V + GS L A AI +G+A + EDR Sbjct: 300 SGNGQSMLAKVLSGLEEPTAGAVTL----GSQPLKANAAA----AIQSGVARIPEDRHHD 351 Query: 359 GLFLDQSVHENINLIVAARDA---LGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGAL 415 G+ SV EN+ L + A GL R N R+R EAI IR + L Sbjct: 352 GIVGAMSVEENLVLEEIRKPAYQRFGLLRFNE--IRKRAQEAIKAYDIRCSGPLAVSRLL 409 Query: 416 SGGNQQKVMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELP 475 SGGN QK++L+R L+ +P +++ +P+RG+D+GA ++++R + G +L+IS +L Sbjct: 410 SGGNIQKIVLARTLDQEPAIVLAAQPSRGLDVGATADVHRRLQEARDRGAGVLLISEDLD 469 Query: 476 EVVGLCDRVLVMREGTLAGEVRPAGSAAETQERIIALATGAAA 518 E+ L DR+ V+ G ++ P S ++++ + G +A Sbjct: 470 ELFQLSDRIAVIHRGHVS---EPMASEELDKKQVGLMMAGHSA 509 Score = 61.6 bits (148), Expect = 7e-14 Identities = 61/237 (25%), Positives = 101/237 (42%), Gaps = 10/237 (4%) Query: 25 GVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECHIDGQRVQIDGPQ 84 G + V L+ GE+ L G +G G+S L K+LSG +P G + Sbjct: 277 GRELIENVNLSLRKGEIIGLAGVSGNGQSMLAKVLSGL--EEPTAGAVTLGSQPLKANAA 334 Query: 85 SARDLGVAVIYQEL---SLAPNLSVAENIYLGR----ALQRRGLVARGDMVRACAPTLAR 137 +A GVA I ++ + +SV EN+ L A QR GL+ ++ + + Sbjct: 335 AAIQSGVARIPEDRHHDGIVGAMSVEENLVLEEIRKPAYQRFGLLRFNEIRKRAQEAIKA 394 Query: 138 LGADFS-PAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFALIRQL 196 S P A LS Q + +AR + E I++ +P+ L T + +++ Sbjct: 395 YDIRCSGPLAVSRLLSGGNIQKIVLARTLDQEPAIVLAAQPSRGLDVGATADVHRRLQEA 454 Query: 197 RGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRDLSG 253 R G +L IS + E+ +L+DR+ V+ G + L + + MM G G Sbjct: 455 RDRGAGVLLISEDLDELFQLSDRIAVIHRGHVSEPMASEELDKKQVGLMMAGHSAKG 511 Lambda K H 0.320 0.136 0.382 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: 583 Number of extensions: 31 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: 540 Length of database: 515 Length adjustment: 35 Effective length of query: 505 Effective length of database: 480 Effective search space: 242400 Effective search space used: 242400 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 (21.8 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