Align m-Inositol ABC transporter, ATPase component (itaA) (characterized)
to candidate Ac3H11_609 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)
Query= reanno::pseudo3_N2E3:AO353_21385 (521 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_609 Length = 505 Score = 379 bits (974), Expect = e-109 Identities = 214/501 (42%), Positives = 317/501 (63%), Gaps = 18/501 (3%) Query: 27 LLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDA--GEL 84 LLE+ N+ K FPGVVAL+ V L+V+ G + A++GENGAGKSTLMK+++G+Y + G++ Sbjct: 2 LLEMRNIRKTFPGVVALNQVNLQVQAGEIHAIVGENGAGKSTLMKVLSGVYPHGSYSGQI 61 Query: 85 RLRGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGFHMIDHREMHRC 144 G+ F + GI +IHQEL L+P +SIAENI++G E +ID H Sbjct: 62 LFDGQEREFAGIRDSEHLGIIIIHQELALVPLLSIAENIFLGNETAR-HGVIDWMAAHSR 120 Query: 145 TAQLLERLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLF 204 LL ++ + P+ VG L + ++Q+VEIAKA+S +LI+DEPT+++ + + L Sbjct: 121 AQALLHKVGLGESPDTPVGQLGVGKQQLVEIAKALSRKVRLLILDEPTASLNENDSQALL 180 Query: 205 SIIADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDG----DSLISMM 260 ++ +LKAQG I I+HK+NE+ +AD + V RDG+ + Q D +G D +I M Sbjct: 181 DLLLELKAQGITCILISHKLNEISRVADAITVLRDGSTV--QMLDCREGPVSEDRVIQAM 238 Query: 261 VGRELSQLFPVREKPIGDLLMSVRDLRLDGV-------FKGVSFDLHAGEILGIAGLMGS 313 VGRE+S +P R+ +G+++ VR+ R KG+ ++ GEI+GIAGLMG+ Sbjct: 239 VGREMSDRYPQRQPQVGEIVFEVRNWRAHHPQRSDREHLKGIDLNVRRGEIVGIAGLMGA 298 Query: 314 GRTNVAEAIFGITPSD--GGEICLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSV 371 GRT +A +IFG + GE+ L GQP+ +S A+ G A +TEDRK +GL + Sbjct: 299 GRTELAMSIFGRSWGQRISGEVRLHGQPIDVSTVEKAVSHGLAYVTEDRKGNGLVLNEDI 358 Query: 372 LENMEMAVLPHYAGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLAR 431 N +A LP + I + +D +KLR++ ++Q LSGGNQQK +L++ Sbjct: 359 QFNTSLANLPGVSFASVIDSGQEHRVAQDYREKLRIRCSGVDQKTLNLSGGNQQKVVLSK 418 Query: 432 WLMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVM 491 WL T+P +LILDEPTRGIDVGAK EIY LI+ LA+EG VI+ISSE+PE+LG++DR+ VM Sbjct: 419 WLFTSPEVLILDEPTRGIDVGAKYEIYTLIAQLAAEGKCVIVISSEMPELLGITDRIYVM 478 Query: 492 HEGDLMGTLDRSEATQERVMQ 512 +EG + + SEA+QE++M+ Sbjct: 479 NEGRFVAEMPTSEASQEKIMR 499 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: 643 Number of extensions: 43 Number of successful extensions: 10 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 521 Length of database: 505 Length adjustment: 35 Effective length of query: 486 Effective length of database: 470 Effective search space: 228420 Effective search space used: 228420 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