Align m-Inositol ABC transporter, ATPase component (itaA) (characterized)
to candidate WP_085124759.1 B9O00_RS21320 sugar ABC transporter ATP-binding protein
Query= reanno::pseudo3_N2E3:AO353_21385 (521 letters) >NCBI__GCF_900177295.1:WP_085124759.1 Length = 518 Score = 350 bits (898), Expect = e-101 Identities = 193/501 (38%), Positives = 292/501 (58%), Gaps = 4/501 (0%) Query: 14 GVQPNAIPVDEPYLLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKII 73 G A P+ LLE+ VS+ FPGV+AL V ++RPG V L GENGAGKST++ +I Sbjct: 10 GPSDRAAPLPAAPLLELRGVSRRFPGVLALDKVDFQLRPGEVHVLFGENGAGKSTMISMI 69 Query: 74 AGIYQPDAGELRLRGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGF 133 AG +P GE R RG+PV ++ A GI+ + QE +L+P M++ EN+++G E Sbjct: 70 AGALRPSEGEFRFRGEPVELNSVHHARGLGISAVFQEFSLVPQMTVEENLFLGAESTR-L 128 Query: 134 HMIDHREMHRCTAQLLERLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTS 193 ++D R +H +L+RL L P ++V +L+ AE+QMVEIAKA + +LI+DEPT+ Sbjct: 129 GLLDRRALHDRADAILKRLGFPLRPRDRVLHLTRAEQQMVEIAKAFRSELSVLILDEPTA 188 Query: 194 AITDKEVAHLFSIIADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDG 253 ++T++E A LF +I +KAQG G+IYITH+++E+ I D + V RDG Y+ A + Sbjct: 189 SLTERETAQLFKLIEQVKAQGVGVIYITHRLSEIRRIGDRITVLRDGRYVATVDAQTTPE 248 Query: 254 DSLISMMVGRELSQLFP-VREKPIGDLLMSVRDLRLDGVFKGVSFDLHAGEILGIAGLMG 312 L+ +M GR +LFP VR KP +LL R G S + AGEI+G+AGL+G Sbjct: 249 GELVRLMTGRVYDELFPKVRFKPGRELLSVERLTTASGSVVEASLSVCAGEIVGLAGLVG 308 Query: 313 SGRTNVAEAIFGITPSDGGEICLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVL 372 SG++ VA A FG+ G + L G+ V P +++GF + DR+ GL V Sbjct: 309 SGKSEVARACFGLEKIAEGHVRLKGEEVTGQGPKRMLKRGFFYVPPDRRDEGLMMMRPVR 368 Query: 373 ENMEM--AVLPHYAGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLA 430 EN+ + L + + ++ + ++L ++ P +E+ ++ SGGNQQK LLA Sbjct: 369 ENVSLPSLTLAPFGNGALLDRRGETDRVRRLAEQLNLQPPRIERAVEAFSGGNQQKVLLA 428 Query: 431 RWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMV 490 + ++ DEPT G+DVG + IY I L G +++ISS+LPEVL +S+R V Sbjct: 429 KSRTRPVQVFAFDEPTVGVDVGTRVAIYEFIRDLCEAGAGILLISSDLPEVLNLSNRAYV 488 Query: 491 MHEGDLMGTLDRSEATQERVM 511 + G + L E T+E+V+ Sbjct: 489 FYRGRVQAELAGDEITEEKVL 509 Score = 84.7 bits (208), Expect = 7e-21 Identities = 56/222 (25%), Positives = 109/222 (49%), Gaps = 6/222 (2%) Query: 295 VSFDLHAGEILGIAGLMGSGRTNVAEAIFGITPSDGGEICLDGQPVRISDPHMAIEKGFA 354 V F L GE+ + G G+G++ + I G GE G+PV ++ H A G + Sbjct: 42 VDFQLRPGEVHVLFGENGAGKSTMISMIAGALRPSEGEFRFRGEPVELNSVHHARGLGIS 101 Query: 355 LLTEDRKLSGLFPCLSVLENMEMAVLPHYAGNGFIQQKALRALCEDMCKKLRVKTPSLEQ 414 + ++ L P ++V EN+ + G + ++AL + + K+L ++ Sbjct: 102 AVFQE---FSLVPQMTVEENLFLGA--ESTRLGLLDRRALHDRADAILKRLGFPLRPRDR 156 Query: 415 CIDTLSGGNQQKALLARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMI 474 + L+ QQ +A+ + +LILDEPT + A++++LI + ++G+ VI I Sbjct: 157 VLH-LTRAEQQMVEIAKAFRSELSVLILDEPTASLTERETAQLFKLIEQVKAQGVGVIYI 215 Query: 475 SSELPEVLGMSDRVMVMHEGDLMGTLDRSEATQERVMQLASG 516 + L E+ + DR+ V+ +G + T+D + +++L +G Sbjct: 216 THRLSEIRRIGDRITVLRDGRYVATVDAQTTPEGELVRLMTG 257 Score = 68.6 bits (166), Expect = 5e-16 Identities = 61/245 (24%), Positives = 109/245 (44%), Gaps = 11/245 (4%) Query: 29 EIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRLRG 88 E+++V + ++ + L V G ++ L G G+GKS + + G+ + G +RL+G Sbjct: 274 ELLSVERLTTASGSVVEASLSVCAGEIVGLAGLVGSGKSEVARACFGLEKIAEGHVRLKG 333 Query: 89 KPVTFDTPLAALQAGIAMI---HQELNLMPHMSIAENIWIGREQLNGFH---MIDHREMH 142 + VT P L+ G + ++ LM + EN+ + L F ++D R Sbjct: 334 EEVTGQGPKRMLKRGFFYVPPDRRDEGLMMMRPVRENVSLPSLTLAPFGNGALLDRRGET 393 Query: 143 RCTAQLLERLRINLDP---EEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKE 199 +L E+L NL P E V S +Q V +AK+ + + DEPT + Sbjct: 394 DRVRRLAEQL--NLQPPRIERAVEAFSGGNQQKVLLAKSRTRPVQVFAFDEPTVGVDVGT 451 Query: 200 VAHLFSIIADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISM 259 ++ I DL G GI+ I+ + EV ++++ VF G D + + ++S Sbjct: 452 RVAIYEFIRDLCEAGAGILLISSDLPEVLNLSNRAYVFYRGRVQAELAGDEITEEKVLSH 511 Query: 260 MVGRE 264 R+ Sbjct: 512 FFERD 516 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: 641 Number of extensions: 25 Number of successful extensions: 8 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: 521 Length of database: 518 Length adjustment: 35 Effective length of query: 486 Effective length of database: 483 Effective search space: 234738 Effective search space used: 234738 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 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