Align m-Inositol ABC transporter, ATPase component (itaA) (characterized)
to candidate RR42_RS32900 RR42_RS32900 sugar ABC transporter ATPase
Query= reanno::pseudo3_N2E3:AO353_21385 (521 letters) >FitnessBrowser__Cup4G11:RR42_RS32900 Length = 502 Score = 376 bits (966), Expect = e-109 Identities = 208/498 (41%), Positives = 303/498 (60%), Gaps = 4/498 (0%) Query: 18 NAIPVDEPYLLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIY 77 NAI P L E+ + K FPGV AL DV + PG V L+GENGAGKS+LMK++ G+Y Sbjct: 2 NAITEITP-LFEMRGICKNFPGVKALDDVSFAIYPGEVHMLLGENGAGKSSLMKVLCGVY 60 Query: 78 QPDAGELRLRGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGFH-MI 136 DAGE G PV +P + GIA+I QE +L+P++ IA+NI++GRE + Sbjct: 61 VADAGEFYHDGSPVAITSPADTMGLGIAVIFQEFSLVPYLDIAQNIFLGREPRGRIPGSV 120 Query: 137 DHREMHRCTAQLLERLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAIT 196 D MH ++L+ L + + V L +A++QMVEIAKA+S ++ IL++DEPT+A++ Sbjct: 121 DAARMHAEARRILDILGMEVSTRTPVHRLGVAQQQMVEIAKALSQNARILVLDEPTAALS 180 Query: 197 DKEVAHLFSIIADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSL 256 D+E LF++IA LKA G +IYI+H+M EVF++ D + + RDG +G D L Sbjct: 181 DRETEKLFAVIARLKADGVSMIYISHRMAEVFALGDRITILRDGRKVGACLPGDATPDEL 240 Query: 257 ISMMVGRELSQLFP-VREKPIGDLLMSVRDLRLDGVFKGVSFDLHAGEILGIAGLMGSGR 315 ++ MVGR++ + R G++ + VR++ D ++ + AGEI+G+AGL+GSGR Sbjct: 241 VARMVGRKVDMSYSRERSAQPGEVALDVRNVSADSGIADINLQVRAGEIVGLAGLVGSGR 300 Query: 316 TNVAEAIFGITPSDGGEICLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENM 375 + VA A+FG P GEI + G+ + P A E G AL+ E RK GL +V +N+ Sbjct: 301 SEVARAVFGADPIRQGEIYIFGKRLT-GGPDRARELGAALIPESRKSEGLALIRTVRDNL 359 Query: 376 EMAVLPHYAGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMT 435 +A L + + AL E +LR+ TP Q LSGGNQQK ++ +WL+ Sbjct: 360 LLAGLRRAFPARWYRADKAEALAEREIARLRIATPDGNQLAQFLSGGNQQKIVIGKWLVA 419 Query: 436 NPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGD 495 ++ I DEPTRGIDVGAKAEI+ LI L +G V++ISSELPE++ + DR VM G Sbjct: 420 EAKLFIFDEPTRGIDVGAKAEIFALIDSLVKQGAGVLLISSELPEIINVCDRTYVMRGGR 479 Query: 496 LMGTLDRSEATQERVMQL 513 + G + +E T+ER++QL Sbjct: 480 IAGEVAHAEMTEERILQL 497 Score = 94.0 bits (232), Expect = 1e-23 Identities = 59/225 (26%), Positives = 113/225 (50%), Gaps = 4/225 (1%) Query: 295 VSFDLHAGEILGIAGLMGSGRTNVAEAIFGITPSDGGEICLDGQPVRISDPHMAIEKGFA 354 VSF ++ GE+ + G G+G++++ + + G+ +D GE DG PV I+ P + G A Sbjct: 29 VSFAIYPGEVHMLLGENGAGKSSLMKVLCGVYVADAGEFYHDGSPVAITSPADTMGLGIA 88 Query: 355 LLTEDRKLSGLFPCLSVLENMEMAVLPHYAGNGFIQQKALRALCEDMCKKLRVKTPSLEQ 414 ++ ++ L P L + +N+ + P G + + A + L ++ S Sbjct: 89 VIFQE---FSLVPYLDIAQNIFLGREPRGRIPGSVDAARMHAEARRILDILGMEV-STRT 144 Query: 415 CIDTLSGGNQQKALLARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMI 474 + L QQ +A+ L N RIL+LDEPT + +++ +I+ L ++G+++I I Sbjct: 145 PVHRLGVAQQQMVEIAKALSQNARILVLDEPTAALSDRETEKLFAVIARLKADGVSMIYI 204 Query: 475 SSELPEVLGMSDRVMVMHEGDLMGTLDRSEATQERVMQLASGMSV 519 S + EV + DR+ ++ +G +G +AT + ++ G V Sbjct: 205 SHRMAEVFALGDRITILRDGRKVGACLPGDATPDELVARMVGRKV 249 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: 687 Number of extensions: 44 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: 502 Length adjustment: 35 Effective length of query: 486 Effective length of database: 467 Effective search space: 226962 Effective search space used: 226962 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 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