Align Inositol transport system ATP-binding protein (characterized)
to candidate Pf1N1B4_410 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)
Query= reanno::WCS417:GFF2332 (517 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_410 Length = 514 Score = 390 bits (1003), Expect = e-113 Identities = 207/493 (41%), Positives = 320/493 (64%), Gaps = 11/493 (2%) Query: 24 LEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRLR 83 L I K FPGV AL + PG V ALMGENGAGKSTL+KI+ G Y P +G++++ Sbjct: 16 LRFNGIGKTFPGVKALDGISFVAHPGQVHALMGENGAGKSTLLKILGGAYTPSSGDLQIG 75 Query: 84 GKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRCTAE 143 + +F++ + +G+A+IHQEL+L+P M++AEN+++G S ++N + + Sbjct: 76 EQKRIFKSTADSIGSGVAVIHQELHLVPEMTVAENLFLGHLPA-SFGLINRGVLRQQALA 134 Query: 144 LLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFSII 203 L L +DP+E+VG LS+ +RQ+VEIAKA+S + ++ DEPTS+++ +E+ L +II Sbjct: 135 CLKGLADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAII 194 Query: 204 ADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIG-LQRADSMNSDSLISMMVGRELS 262 L+ +GK ++Y++H+M EVF I + V VF+DG ++ + ++ D L++ MVGR++ Sbjct: 195 GRLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRFVRTFEDMSALTHDQLVTCMVGRDIQ 254 Query: 263 QLFPLRETPIGDLLLTVRDLTLDGVFKDVSFDLHAGEILGIAGLMGSGRTNVAETIFGIT 322 ++ R P G + L V L G+ + VSF+ H GEILG+ GL+G+GRT + + G+T Sbjct: 255 DIYDYRSRPRGAVALKVDGLLGPGLREPVSFEAHKGEILGLFGLVGAGRTELFRMLSGLT 314 Query: 323 PSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYTGN 382 +++G++ L G+ +++ P AI G L EDRK G+ P SV EN+ ++ ++ Sbjct: 315 RNTAGRLELRGRELKLHSPRDAIAAGILLCPEDRKKEGILPLASVAENINISARGAHSTF 374 Query: 383 GFIQQKALRALCED-----MCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLLI 437 G + LR L E K L+VKTP+ Q I LSGGNQQKA+L RWL ++L+ Sbjct: 375 GCL----LRGLWEKDNADKQIKALKVKTPNAAQKIMYLSGGNQQKAILGRWLSMPMKVLL 430 Query: 438 LDEPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLD 497 LDEPTRGID+GAKAEIY++I LA+ G+AVI++SS+L EV+G+SDR++V+ EG + G L Sbjct: 431 LDEPTRGIDIGAKAEIYQIIHNLAASGIAVIVVSSDLMEVMGISDRILVLCEGAMRGELT 490 Query: 498 RSEATQEKVMQLA 510 R +A + ++QLA Sbjct: 491 REQANESNLLQLA 503 Score = 82.0 bits (201), Expect = 5e-20 Identities = 56/225 (24%), Positives = 107/225 (47%), Gaps = 6/225 (2%) Query: 42 VQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRLRGKPIVFETPLAAQKAGIA 101 V G +L L G GAG++ L ++++G+ + AG + LRG+ + +P A AGI Sbjct: 283 VSFEAHKGEILGLFGLVGAGRTELFRMLSGLTRNTAGRLELRGRELKLHSPRDAIAAGIL 342 Query: 102 MIHQELN---LMPHMSIAENIWIGREQLNSLHMVNHR---EMHRCTAELLARLRINLDPE 155 + ++ ++P S+AENI I +S R E ++ A + Sbjct: 343 LCPEDRKKEGILPLASVAENINISARGAHSTFGCLLRGLWEKDNADKQIKALKVKTPNAA 402 Query: 156 EQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFSIIADLKSQGKGIVY 215 +++ LS +Q + + +S +L++DEPT I A ++ II +L + G ++ Sbjct: 403 QKIMYLSGGNQQKAILGRWLSMPMKVLLLDEPTRGIDIGAKAEIYQIIHNLAASGIAVIV 462 Query: 216 ITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGRE 260 ++ + EV I+D + V +G G + N +L+ + + R+ Sbjct: 463 VSSDLMEVMGISDRILVLCEGAMRGELTREQANESNLLQLALPRQ 507 Lambda K H 0.320 0.136 0.381 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: 627 Number of extensions: 29 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 517 Length of database: 514 Length adjustment: 35 Effective length of query: 482 Effective length of database: 479 Effective search space: 230878 Effective search space used: 230878 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