Align Inositol transport ATP-binding protein IatA, component of The myoinositol (high affinity)/ D-ribose (low affinity) transporter IatP/IatA/IbpA. The structure of IbpA with myoinositol bound has been solved (characterized)
to candidate Ac3H11_609 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)
Query= TCDB::B8H229 (515 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_609 Length = 505 Score = 363 bits (931), Expect = e-104 Identities = 208/500 (41%), Positives = 314/500 (62%), Gaps = 10/500 (2%) Query: 3 LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAA--HAADAGTV 60 LL++ + K+FPGV AL+QV+L V GE+HA++GENGAGKSTL+K+LS H + +G + Sbjct: 2 LLEMRNIRKTFPGVVALNQVNLQVQAGEIHAIVGENGAGKSTLMKVLSGVYPHGSYSGQI 61 Query: 61 TFAGQVLDPRDAPLR-RQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRA 119 F GQ + A +R + LGI I+QE L P LS+AEN++LG E R G++DW + Sbjct: 62 LFDGQ--EREFAGIRDSEHLGIIIIHQELALVPLLSIAENIFLGNETARHGVIDWMAAHS 119 Query: 120 DAQALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRL 179 AQALL+ +GL +PD PV L V +QQ+VEIAKA++ RL+I+DEPTA+L+ + L Sbjct: 120 RAQALLHKVGLGESPDTPVGQLGVGKQQLVEIAKALSRKVRLLILDEPTASLNENDSQAL 179 Query: 180 HAIIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVAD--MVRLMV 237 ++ LKA+ ++ I +SH+L E+ + D TV+RDG V D + V++ +++ MV Sbjct: 180 LDLLLELKAQGITCILISHKLNEISRVADAITVLRDGSTVQMLDCREGPVSEDRVIQAMV 239 Query: 238 GRHVEFERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAG 297 GR + +R+ G +V +V P+ S +L+ + R GEIVG+AGL+GAG Sbjct: 240 GREMSDRYPQRQPQVGEIVFEVRNWRAHHPQRSDREHLKGIDLNVRRGEIVGIAGLMGAG 299 Query: 298 RTDLARLIFGAD--PIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIR 355 RT+LA IFG +G V + +P+ + + A+ G+ V EDRK G L+ I+ Sbjct: 300 RTELAMSIFGRSWGQRISGEVRLHGQPIDVSTVEKAVSHGLAYVTEDRKGNGLVLNEDIQ 359 Query: 356 RNLSLPSLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGR 415 N SL +L +S +D E + + YR+KLRI+ + + LSGGNQQKV+L + Sbjct: 360 FNTSLANLPGVS-FASVIDSGQEHRVAQDYREKLRIRCSGVDQKTLNLSGGNQQKVVLSK 418 Query: 416 AMALTPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVF 475 + +P+VLI+DEPTRGID+GAK E++ +++ LA G V+VISSE+ E++ ++DRI V Sbjct: 419 WLFTSPEVLILDEPTRGIDVGAKYEIYTLIAQLAAEGKCVIVISSEMPELLGITDRIYVM 478 Query: 476 REGVIVADLDAQTATEEGLM 495 EG VA++ A++E +M Sbjct: 479 NEGRFVAEMPTSEASQEKIM 498 Score = 54.3 bits (129), Expect = 1e-11 Identities = 56/227 (24%), Positives = 97/227 (42%), Gaps = 9/227 (3%) Query: 19 LDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAAD--AGTVTFAGQVLDPRDAPLRR 76 L +DL V GE+ + G GAG++ L + +G V GQ +D + Sbjct: 277 LKGIDLNVRRGEIVGIAGLMGAGRTELAMSIFGRSWGQRISGEVRLHGQPIDVSTVE-KA 335 Query: 77 QQLGIATIYQEFN---LFPELSVAENMYLGREP--RRLGLVDWSRLRADAQALLNDLGLP 131 G+A + ++ L + N L P ++D + AQ L + Sbjct: 336 VSHGLAYVTEDRKGNGLVLNEDIQFNTSLANLPGVSFASVIDSGQEHRVAQDYREKLRIR 395 Query: 132 LNP-DAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAIIAGLKARS 190 + D L+ QQ V ++K + + ++I+DEPT + ++ +IA L A Sbjct: 396 CSGVDQKTLNLSGGNQQKVVLSKWLFTSPEVLILDEPTRGIDVGAKYEIYTLIAQLAAEG 455 Query: 191 VSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMV 237 VI +S + E+ + DR VM +GRFVA ++ ++R +V Sbjct: 456 KCVIVISSEMPELLGITDRIYVMNEGRFVAEMPTSEASQEKIMRAIV 502 Lambda K H 0.320 0.136 0.380 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: 640 Number of extensions: 30 Number of successful extensions: 8 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: 515 Length of database: 505 Length adjustment: 34 Effective length of query: 481 Effective length of database: 471 Effective search space: 226551 Effective search space used: 226551 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