Align m-Inositol ABC transporter, ATPase component (itaA) (characterized)
to candidate 206505 DVU1070 branched chain amino acid ABC transporter, ATP-binding protein (TIGR)
Query= reanno::pseudo3_N2E3:AO353_21385 (521 letters) >FitnessBrowser__DvH:206505 Length = 524 Score = 286 bits (732), Expect = 1e-81 Identities = 177/506 (34%), Positives = 285/506 (56%), Gaps = 17/506 (3%) Query: 8 SSIPLVGVQPNAIPVDEPYLLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKS 67 S+ P G A+ D ++ + + K F V A D+ L + PG + AL+GENGAGKS Sbjct: 15 STTPQTGRTGRALRHDVTPVVRLEGIGKSFGPVRANHDITLDIVPGRIKALLGENGAGKS 74 Query: 68 TLMKIIAGIYQPDAGELRLRGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGR 127 TLM I++G D G + + G+ V F +P AL+AGI M++Q L+ M++AEN+ +G+ Sbjct: 75 TLMSILSGRLAQDTGIIHVDGEAVRFRSPKDALKAGIGMVYQHFMLVDSMTVAENVLLGQ 134 Query: 128 EQLNGFHMIDHREMHRCTAQLLERLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILI 187 + M R A+L R +++DP +V +LS+ ERQ VEI K + DS +LI Sbjct: 135 SGA----WLSPVHMSRVVAELAARYGLDIDPAARVCDLSMGERQRVEILKLLYRDSRVLI 190 Query: 188 MDEPTSAITDKEVAHLFSIIADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQR 247 +DEPT+ +T E LF + + GK I++I+HKM EV ++ADE+A+ R G + Sbjct: 191 LDEPTAVLTPGETEQLFEALHRMAENGKAIVFISHKMQEVLALADEIAILRRGEVVDEFH 250 Query: 248 ADSMDGDS-LISMMVGRELSQLFPVREKPI--GDLLMSVRDLRLDGVFKGVSFDLHAGEI 304 + G++ L + MVGRE+ + V +P+ GD ++ V L DG+ KG+SF++ GE+ Sbjct: 251 ESEVPGEAELANRMVGREV--ILEVAAEPLEPGDRVLHVDGLAGDGL-KGLSFEVRKGEV 307 Query: 305 LGIAGLMGSGRTNVAEAIFGITPSDGGEICLDGQPVRISDPHMAIEKGFALLTEDRKLSG 364 IAG+ G+G+ + E + G+ GE+ L G P R + G A + EDR+ G Sbjct: 308 FAIAGVAGNGQRELVECVTGLRRPAEGEVELLGIPWRQFFTKAPRQGGLAYIPEDRQ--G 365 Query: 365 LFPCLS--VLENMEMAVLPHYAGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGG 422 L CLS +++N + + F+ +K+ A D+ + V+ E +LSGG Sbjct: 366 LATCLSLDLVDNFLLTARGCFTRGPFLDRKSADAAARDILAEYNVQPGRAEAPARSLSGG 425 Query: 423 NQQKALLARWLMTNPRILILDEPTRGIDVGAKAEIY-RLISYLASEGMAVIMISSELPEV 481 N QK ++ R P +++ + PT+G+D+ A E++ RL+ + G V+++S +L EV Sbjct: 426 NLQKLVVGREFYRKPSLIVAENPTQGLDIAATEEVWARLLEVRSHAG--VLLVSGDLNEV 483 Query: 482 LGMSDRVMVMHEGDLMGTLDRSEATQ 507 L ++DRV VM+ G +G LDRS+ + Sbjct: 484 LALADRVAVMYRGCFIGLLDRSDTNK 509 Score = 81.6 bits (200), Expect = 6e-20 Identities = 59/232 (25%), Positives = 108/232 (46%), Gaps = 18/232 (7%) Query: 286 LRLDGVFKG---------VSFDLHAGEILGIAGLMGSGRTNVAEAIFGITPSDGGEICLD 336 +RL+G+ K ++ D+ G I + G G+G++ + + G D G I +D Sbjct: 35 VRLEGIGKSFGPVRANHDITLDIVPGRIKALLGENGAGKSTLMSILSGRLAQDTGIIHVD 94 Query: 337 GQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYAGNGFIQQKALRA 396 G+ VR P A++ G ++ + L ++V EN VL +G R Sbjct: 95 GEAVRFRSPKDALKAGIGMVYQHFML---VDSMTVAEN----VLLGQSGAWLSPVHMSRV 147 Query: 397 LCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILILDEPTRGIDVGAKAE 456 + E + P+ C LS G +Q+ + + L + R+LILDEPT + G + Sbjct: 148 VAELAARYGLDIDPAARVC--DLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPGETEQ 205 Query: 457 IYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLDRSEATQE 508 ++ + +A G A++ IS ++ EVL ++D + ++ G+++ SE E Sbjct: 206 LFEALHRMAENGKAIVFISHKMQEVLALADEIAILRRGEVVDEFHESEVPGE 257 Score = 67.0 bits (162), Expect = 2e-15 Identities = 55/228 (24%), Positives = 102/228 (44%), Gaps = 11/228 (4%) Query: 43 LSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRLRGKPVTFDTPLAALQA 102 L + VR G V A+ G G G+ L++ + G+ +P GE+ L G P A Q Sbjct: 295 LKGLSFEVRKGEVFAIAGVAGNGQRELVECVTGLRRPAEGEVELLGIPWRQFFTKAPRQG 354 Query: 103 GIAMI---HQELNLMPHMSIAENIWI-GREQLNGFHMIDHREMHRCTAQLLERLRINLDP 158 G+A I Q L + + +N + R +D + +L N+ P Sbjct: 355 GLAYIPEDRQGLATCLSLDLVDNFLLTARGCFTRGPFLDRKSADAAARDILAEY--NVQP 412 Query: 159 ---EEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLFSIIADLKAQGK 215 E +LS Q + + + +++ + PT + +++ + ++++ Sbjct: 413 GRAEAPARSLSGGNLQKLVVGREFYRKPSLIVAENPTQGLDIAATEEVWARLLEVRSHA- 471 Query: 216 GIIYITHKMNEVFSIADEVAVFRDGAYIG-LQRADSMDGDSLISMMVG 262 G++ ++ +NEV ++AD VAV G +IG L R+D+ D++ MM G Sbjct: 472 GVLLVSGDLNEVLALADRVAVMYRGCFIGLLDRSDTNKVDAIGLMMAG 519 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: 624 Number of extensions: 38 Number of successful extensions: 8 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: 524 Length adjustment: 35 Effective length of query: 486 Effective length of database: 489 Effective search space: 237654 Effective search space used: 237654 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