Align m-Inositol ABC transporter, ATPase component (itaA) (characterized)
to candidate SMc02325 SMc02325 ABC transporter ATP-binding protein
Query= reanno::pseudo3_N2E3:AO353_21385 (521 letters) >FitnessBrowser__Smeli:SMc02325 Length = 503 Score = 430 bits (1105), Expect = e-125 Identities = 216/488 (44%), Positives = 327/488 (67%) Query: 33 VSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRLRGKPVT 92 +SK FPGV ALSDV L + PGSV AL+GENGAGKSTL+KI+ GIYQPDAG +RL T Sbjct: 10 ISKSFPGVRALSDVSLALYPGSVTALVGENGAGKSTLVKILTGIYQPDAGTIRLGDTETT 69 Query: 93 FDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGFHMIDHREMHRCTAQLLERL 152 F T LAA +AG+ IHQE L +S+AENI++G N F +ID ++++ LL R Sbjct: 70 FPTALAASRAGVTAIHQETVLFDELSVAENIFLGHAPRNRFGLIDWKQLNADAQALLGRA 129 Query: 153 RINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLFSIIADLKA 212 + DP ++ +L IA++ +V IA+A+S D+ ++IMDEPT+A++ KE+ L+ +I LKA Sbjct: 130 GADFDPTIRLRDLGIAKKHLVAIARALSVDARVVIMDEPTAALSHKEIHELYDLIERLKA 189 Query: 213 QGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGRELSQLFPVR 272 GK +++I+HK +E+F IAD VFRDGA IG + D L+ MMVGR + ++P + Sbjct: 190 DGKAVLFISHKFDEIFRIADRYTVFRDGAMIGEGLIADVSQDDLVRMMVGRAVGSVYPKK 249 Query: 273 EKPIGDLLMSVRDLRLDGVFKGVSFDLHAGEILGIAGLMGSGRTNVAEAIFGITPSDGGE 332 E IG +++V R F+ ++F+L GEILG GL+G+GR+ +++ GIT G Sbjct: 250 EVTIGQPVLTVSGYRHPTEFEDINFELRRGEILGFYGLVGAGRSEFMQSLIGITRPSAGA 309 Query: 333 ICLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYAGNGFIQQK 392 + LDG+ + I P AI G + E+R G + + +N+ + L H + +GF++ Sbjct: 310 VKLDGEVLVIRSPAEAIRAGIVYVPEERGRQGAIIGMPIFQNVTLPSLSHTSRSGFLRLA 369 Query: 393 ALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILILDEPTRGIDVG 452 AL + +L ++ +L+Q + TLSGGNQQK ++A+WL T P+++ILDEPT+GID+G Sbjct: 370 EEFALAREYTSRLDLRAAALDQDVGTLSGGNQQKVVIAKWLATRPKVIILDEPTKGIDIG 429 Query: 453 AKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLDRSEATQERVMQ 512 +KA ++ +S LA++G++VIM+SSE+PE++GMSDRV+VM EG + G +RSE T E++++ Sbjct: 430 SKAAVHAFMSELAAQGLSVIMVSSEIPEIMGMSDRVIVMREGRVAGRYERSELTAEKLVR 489 Query: 513 LASGMSVR 520 A+G+ + Sbjct: 490 AAAGIETQ 497 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: 622 Number of extensions: 28 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 521 Length of database: 503 Length adjustment: 35 Effective length of query: 486 Effective length of database: 468 Effective search space: 227448 Effective search space used: 227448 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