Align m-Inositol ABC transporter, ATPase component (itaA) (characterized)
to candidate Pf6N2E2_1008 Inositol transport system ATP-binding protein
Query= reanno::pseudo3_N2E3:AO353_21385 (521 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1008 Length = 485 Score = 347 bits (891), Expect = e-100 Identities = 204/478 (42%), Positives = 298/478 (62%), Gaps = 19/478 (3%) Query: 58 LMGENGAGKSTLMKIIAGIYQPDAGE--LRLRGKPV-TFDTPLAALQAGIAMIHQELNLM 114 L+GENGAGKST++KI+AG DAG+ L G + DTP+ + GI I+QE NL+ Sbjct: 1 LLGENGAGKSTILKILAGAQPADAGQGSLEFNGHVLGEHDTPIRRQEVGIITIYQEFNLI 60 Query: 115 PHMSIAENIWIGREQL-NGFHMIDHREMHRCTAQLLERLRINLDPEEQVGNLSIAERQMV 173 MS+AEN+++GRE L +GF +D ++M +L+ L +++ P V LS+AE+QMV Sbjct: 61 ADMSVAENMYLGREPLRHGF--VDWKQMFSDAQHVLDDLGLHITPRTMVRKLSVAEQQMV 118 Query: 174 EIAKAVSYDSDILIMDEPTSAITDKEVAHLFSIIADLKAQGKGIIYITHKMNEVFSIADE 233 EIAKA++ ++ ++IMDEPT+A++ +EV L II DLKA+G IIY++HK+NEV + D Sbjct: 119 EIAKALTMNAKLIIMDEPTAALSGREVDKLHEIITDLKAKGISIIYVSHKLNEVKACCDR 178 Query: 234 VAVFRDGAYIGLQRADSMDGDSLISMMVGRELSQLFPVREKPIGDLLMSVRDLRLDGVFK 293 +FRDGAYI + D ++ +MVGR++ + G++++ V+ + Sbjct: 179 YTIFRDGAYITSGDVCDVSVDDIVRLMVGRDVEFVRKPLTGAPGEVMLKVQSVSRTAAGG 238 Query: 294 G----------VSFDLHAGEILGIAGLMGSGRTNVAEAIFGITPSDGGEICLDGQPVR-I 342 G +S D+ AGEI+G AGL+G+GRT +A IFG D G I ++G+ V Sbjct: 239 GRSLHATPLLDMSVDVRAGEIVGFAGLVGAGRTELARVIFGADGCDEGMIYVNGRQVSPF 298 Query: 343 SDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYAGNG-FIQQKALRALCEDM 401 P I G AL+ EDRK F S+ NM + L G FI +A L +D Sbjct: 299 KSPREGIAAGVALVPEDRKQQACFLSHSIRWNMSLPSLGGLQRWGMFIDDRAETQLIQDY 358 Query: 402 CKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILILDEPTRGIDVGAKAEIYRLI 461 K+LR+K + I TLSGGNQQK +LAR + P++LI+DEPTRGIDVGAKAE+++L+ Sbjct: 359 QKRLRIKMSNDSVAIGTLSGGNQQKVILARCMALKPKVLIVDEPTRGIDVGAKAEVHQLL 418 Query: 462 SYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLDRSEATQERVM-QLASGMS 518 +A G+AVI+ISSELPEV+ +SDR++ EG + G + EAT+E +M ++A G+S Sbjct: 419 FDMARAGVAVIVISSELPEVMAVSDRIVTFREGQITGIVSADEATEELLMARMAQGVS 476 Score = 89.7 bits (221), Expect = 2e-22 Identities = 68/250 (27%), Positives = 123/250 (49%), Gaps = 19/250 (7%) Query: 27 LLEIINVSKGFPG------VVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPD 80 +L++ +VS+ G L D+ + VR G ++ G GAG++ L ++I G D Sbjct: 225 MLKVQSVSRTAAGGGRSLHATPLLDMSVDVRAGEIVGFAGLVGAGRTELARVIFGADGCD 284 Query: 81 AGELRLRGKPVT-FDTPLAALQAGIAMI----HQELNLMPHMSIAENIWIGREQLNGFH- 134 G + + G+ V+ F +P + AG+A++ Q+ + H SI N+ + L G Sbjct: 285 EGMIYVNGRQVSPFKSPREGIAAGVALVPEDRKQQACFLSH-SIRWNMSL--PSLGGLQR 341 Query: 135 ---MIDHREMHRCTAQLLERLRINLDPEE-QVGNLSIAERQMVEIAKAVSYDSDILIMDE 190 ID R + +RLRI + + +G LS +Q V +A+ ++ +LI+DE Sbjct: 342 WGMFIDDRAETQLIQDYQKRLRIKMSNDSVAIGTLSGGNQQKVILARCMALKPKVLIVDE 401 Query: 191 PTSAITDKEVAHLFSIIADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADS 250 PT I A + ++ D+ G +I I+ ++ EV +++D + FR+G G+ AD Sbjct: 402 PTRGIDVGAKAEVHQLLFDMARAGVAVIVISSELPEVMAVSDRIVTFREGQITGIVSADE 461 Query: 251 MDGDSLISMM 260 + L++ M Sbjct: 462 ATEELLMARM 471 Score = 64.3 bits (155), Expect = 1e-14 Identities = 49/214 (22%), Positives = 103/214 (48%), Gaps = 5/214 (2%) Query: 307 IAGLMGSGRTNVAEAIFGITPSDGGEICLDGQPVRISDPHMAIEKGFALLTEDRKLSGLF 366 + G G+G++ + + + G P+D G+ L+ + + I + + + L Sbjct: 1 LLGENGAGKSTILKILAGAQPADAGQGSLEFNGHVLGEHDTPIRRQEVGIITIYQEFNLI 60 Query: 367 PCLSVLENMEMAVLPHYAGNGFIQQKALRALCEDMCKKLRVK-TPSLEQCIDTLSGGNQQ 425 +SV ENM + P +GF+ K + + + + L + TP + LS QQ Sbjct: 61 ADMSVAENMYLGREP--LRHGFVDWKQMFSDAQHVLDDLGLHITP--RTMVRKLSVAEQQ 116 Query: 426 KALLARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMS 485 +A+ L N +++I+DEPT + +++ +I+ L ++G+++I +S +L EV Sbjct: 117 MVEIAKALTMNAKLIIMDEPTAALSGREVDKLHEIITDLKAKGISIIYVSHKLNEVKACC 176 Query: 486 DRVMVMHEGDLMGTLDRSEATQERVMQLASGMSV 519 DR + +G + + D + + + +++L G V Sbjct: 177 DRYTIFRDGAYITSGDVCDVSVDDIVRLMVGRDV 210 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: 644 Number of extensions: 31 Number of successful extensions: 10 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: 485 Length adjustment: 34 Effective length of query: 487 Effective length of database: 451 Effective search space: 219637 Effective search space used: 219637 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