Align m-Inositol ABC transporter, ATPase component (itaA) (characterized)
to candidate WP_068000812.1 PsAD2_RS00245 ABC transporter ATP-binding protein
Query= reanno::pseudo3_N2E3:AO353_21385 (521 letters) >NCBI__GCF_001623255.1:WP_068000812.1 Length = 514 Score = 299 bits (765), Expect = 2e-85 Identities = 180/506 (35%), Positives = 288/506 (56%), Gaps = 22/506 (4%) Query: 28 LEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRLR 87 +E+I V+K F V A D+ L V GS+ ++GENGAGKSTLM I+ G Y D+G +++ Sbjct: 9 IELIGVNKSFGPVHANKDIDLVVGKGSIHGIIGENGAGKSTLMSILYGFYHADSGTIKID 68 Query: 88 GKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGFHMID-----HREMH 142 GK T +A+ GI M+HQ L+ ++ EN+ +G E G + D RE+ Sbjct: 69 GKATTIPDSKSAISQGIGMVHQHFMLVDPFTVLENVVLGAE--GGALLKDGVANARRELK 126 Query: 143 RCTAQLLERLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAH 202 R L + + +DP+ VG L + +Q VEI KA+ +DILI+DEPT +T E H Sbjct: 127 R----LADEYDMTIDPDAVVGELPVGLQQRVEILKALYRGADILILDEPTGVLTPSEADH 182 Query: 203 LFSIIADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMMVG 262 LF I+ L+ QGK ++ ITHK+ E+ + D V+V R G + ++ + L +MVG Sbjct: 183 LFRILRVLRDQGKTVLLITHKLREIMDVTDTVSVMRRGEMVASRKTAQTSMEELAELMVG 242 Query: 263 RELSQLFPVREKPIGDLLMSVRDLRLD---GV--FKGVSFDLHAGEILGIAGLMGSGRTN 317 R + + +G L+ V L + GV K VSF++ AGE+LGIAG+ G+G++ Sbjct: 243 RSVLLEVSKPDVEVGKPLLKVEGLNVKDERGVRRVKDVSFEVRAGEVLGIAGVSGNGQSE 302 Query: 318 VAEAIFGITPSDGGEICLDGQPVRISDPHMAI---EKGFALLTEDRKLSGLFPCLSVLEN 374 + A+ GIT ++ G + L GQ + +S+ H A ++G + + EDR GL S EN Sbjct: 303 LMAALAGITRAESGSMELAGQKLDLSEVHDAAQMRDRGMSHVPEDRHRMGLVNKFSEAEN 362 Query: 375 MEMAV--LPHYAGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARW 432 + Y+ F+ + A+R ++ +K ++ P E SGGNQQK +LAR Sbjct: 363 SILGYHRESKYSKGMFLDKDAIRKEAKERIEKYDIRPPLTEMTAAKFSGGNQQKIVLARE 422 Query: 433 LMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMH 492 + NP +L++ +PTRG+D+GA I+ I + ++G AV+++S EL E+ +SDR++VM Sbjct: 423 IECNPDVLLIGQPTRGVDIGAIEYIHNRIMDMRAQGKAVLLVSVELDEIRSLSDRIIVMF 482 Query: 493 EGDLMGTLDRSEATQERVMQLASGMS 518 +G+++G EAT++ + L +G++ Sbjct: 483 DGNVVGERG-PEATEQDLGLLMAGVN 507 Score = 85.1 bits (209), Expect = 6e-21 Identities = 61/230 (26%), Positives = 111/230 (48%), Gaps = 12/230 (5%) Query: 293 KGVSFDLHAGEILGIAGLMGSGRTNVAEAIFGITPSDGGEICLDGQPVRISDPHMAIEKG 352 K + + G I GI G G+G++ + ++G +D G I +DG+ I D AI +G Sbjct: 25 KDIDLVVGKGSIHGIIGENGAGKSTLMSILYGFYHADSGTIKIDGKATTIPDSKSAISQG 84 Query: 353 FALLTEDRKLSGLFPCLSVLENMEMAVLPHYAGNGFIQQKALRALCEDMCKKLRVK---T 409 ++ + L F +VLEN+ + G ++ A E K+L + T Sbjct: 85 IGMVHQHFMLVDPF---TVLENVVLGA----EGGALLKDGVANARRE--LKRLADEYDMT 135 Query: 410 PSLEQCIDTLSGGNQQKALLARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGM 469 + + L G QQ+ + + L ILILDEPT + ++R++ L +G Sbjct: 136 IDPDAVVGELPVGLQQRVEILKALYRGADILILDEPTGVLTPSEADHLFRILRVLRDQGK 195 Query: 470 AVIMISSELPEVLGMSDRVMVMHEGDLMGTLDRSEATQERVMQLASGMSV 519 V++I+ +L E++ ++D V VM G+++ + ++ + E + +L G SV Sbjct: 196 TVLLITHKLREIMDVTDTVSVMRRGEMVASRKTAQTSMEELAELMVGRSV 245 Lambda K H 0.321 0.137 0.391 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: 637 Number of extensions: 31 Number of successful extensions: 8 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: 521 Length of database: 514 Length adjustment: 35 Effective length of query: 486 Effective length of database: 479 Effective search space: 232794 Effective search space used: 232794 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