Align m-Inositol ABC transporter, ATPase component (itaA) (characterized)
to candidate Ac3H11_607 Predicted L-arabinose ABC transport system, ATP-binding protein
Query= reanno::pseudo3_N2E3:AO353_21385 (521 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_607 Length = 517 Score = 361 bits (927), Expect = e-104 Identities = 197/493 (39%), Positives = 308/493 (62%), Gaps = 15/493 (3%) Query: 17 PNAIPVDEPYLLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGI 76 P A PV L++ + K F G+ L DVQL + PG + ALMG+NGAGKSTL+K++ G+ Sbjct: 13 PAAAPV-----LQLSGIHKQFAGITVLRDVQLNLYPGEIHALMGQNGAGKSTLIKVLTGV 67 Query: 77 YQPDAGELRLRGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGFHM- 135 + G++RL G+ V D+PLAA + GI+ ++QE+NL P++S+AENI+ GR G Sbjct: 68 LEASGGQMRLGGQAVWPDSPLAAQRLGISTVYQEVNLCPNLSVAENIFAGRYPRCGIAQG 127 Query: 136 --IDHREMHRCTAQLLERLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTS 193 ID +H+ L+ R+ + +D + + +A +Q+V IA+A+S +S +LI+DEPTS Sbjct: 128 FRIDWATLHQRARDLVARIGLQIDVTRLLSDYPVAVQQLVAIARALSIESRVLILDEPTS 187 Query: 194 AITDKEVAHLFSIIADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDG 253 ++ D EV LF ++ L+++G I+++TH +N+V++++D + V R+G+++G A + Sbjct: 188 SLDDDEVQKLFEVLRRLRSEGLSIVFVTHFLNQVYAVSDRITVLRNGSWVGEWLAKDLGP 247 Query: 254 DSLISMMVGRELSQLF------PVREKPIGDLLMSVRDLRLDGVFKGVSFDLHAGEILGI 307 +LI+ M+GR+L+ P + +LL + L D + + + AGE++G+ Sbjct: 248 QALIAAMLGRDLAAASEQPAPAPAVDSRHANLLQA-EGLGQDTQLQPLDLQIRAGEVVGL 306 Query: 308 AGLMGSGRTNVAEAIFGITPSDGGEICLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFP 367 AGL+GSGRT +A +FG+ D G + +DGQ V+ ++P AI G AL E+RK G+ Sbjct: 307 AGLLGSGRTELARLLFGLEQPDRGALRIDGQVVKFANPMDAIRHGLALCPEERKTDGIVA 366 Query: 368 CLSVLENMEMAVLPHYAGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKA 427 LSV EN+ +A+ F+ + L E K L +KT ++++ I LSGGNQQKA Sbjct: 367 ELSVRENIALALQARMGVGKFLSRSEQTELAERYVKLLGIKTETVDKPIGLLSGGNQQKA 426 Query: 428 LLARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDR 487 +LARW+ PR+LILDEPTRGIDV AK EI I LA GMAV+ ISSE+ EV+ ++ R Sbjct: 427 ILARWMAIEPRLLILDEPTRGIDVAAKQEIMDQILRLAQAGMAVLFISSEMSEVVRVAHR 486 Query: 488 VMVMHEGDLMGTL 500 ++V+ + +G L Sbjct: 487 IVVLRDRRKVGEL 499 Score = 94.0 bits (232), Expect = 1e-23 Identities = 64/257 (24%), Positives = 124/257 (48%), Gaps = 6/257 (2%) Query: 1 MFASATASSIPLVGVQPNAIPVDEPYLLEIINVSKGFPGVVALSDVQLRVRPGSVLALMG 60 + A+ + QP P + ++ ++G L + L++R G V+ L G Sbjct: 250 LIAAMLGRDLAAASEQPAPAPAVDSRHANLLQ-AEGLGQDTQLQPLDLQIRAGEVVGLAG 308 Query: 61 ENGAGKSTLMKIIAGIYQPDAGELRLRGKPVTFDTPLAALQAGIAMIHQELN---LMPHM 117 G+G++ L +++ G+ QPD G LR+ G+ V F P+ A++ G+A+ +E ++ + Sbjct: 309 LLGSGRTELARLLFGLEQPDRGALRIDGQVVKFANPMDAIRHGLALCPEERKTDGIVAEL 368 Query: 118 SIAENIWIGREQLNGF-HMIDHREMHRCTAQLLERLRINLDP-EEQVGNLSIAERQMVEI 175 S+ ENI + + G + E + ++ L I + ++ +G LS +Q + Sbjct: 369 SVRENIALALQARMGVGKFLSRSEQTELAERYVKLLGIKTETVDKPIGLLSGGNQQKAIL 428 Query: 176 AKAVSYDSDILIMDEPTSAITDKEVAHLFSIIADLKAQGKGIIYITHKMNEVFSIADEVA 235 A+ ++ + +LI+DEPT I + I L G +++I+ +M+EV +A + Sbjct: 429 ARWMAIEPRLLILDEPTRGIDVAAKQEIMDQILRLAQAGMAVLFISSEMSEVVRVAHRIV 488 Query: 236 VFRDGAYIGLQRADSMD 252 V RD +G A S + Sbjct: 489 VLRDRRKVGELPAGSSE 505 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: 620 Number of extensions: 24 Number of successful extensions: 7 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: 517 Length adjustment: 35 Effective length of query: 486 Effective length of database: 482 Effective search space: 234252 Effective search space used: 234252 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