Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate CCNA_00903 CCNA_00903 inositol transport ATP-binding protein IatA
Query= TCDB::P0AAG8 (506 letters) >FitnessBrowser__Caulo:CCNA_00903 Length = 515 Score = 360 bits (924), Expect = e-104 Identities = 189/493 (38%), Positives = 310/493 (62%), Gaps = 6/493 (1%) Query: 13 LLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTILF 72 LL++S ++KSFPGV+ALD V+L V +HAL+GENGAGKSTL+K L + D+GT+ F Sbjct: 3 LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62 Query: 73 QGKEIDFHSAKEALEN-GISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKMYRETK 131 G+ +D A + GI+ ++QE NL + SV +NM+LGR P + VD ++ + + Sbjct: 63 AGQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRADAQ 122 Query: 132 AIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTI 191 A+ ++L + ++P A V L+V++ QM+EIAKA + NA+++IMDEPT++L+ +EV+ L I Sbjct: 123 ALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAI 182 Query: 192 IRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRSLN 251 I LK R ++Y+SH++ E+ +CD TV+RDG+++A+ +A + + ++ +MVGR + Sbjct: 183 IAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHVE 242 Query: 252 QRFPDKENKPGEVILEVRNLT----SLRQPS-IRDVSFDLHKGEILGIAGLVGAKRTDIV 306 + PG V+L+V +T L P +R VSF GEI+G+AGLVGA RTD+ Sbjct: 243 FERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLA 302 Query: 307 ETLFGIREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLISN 366 +FG +AG + + K + + +AI G LV E+R+ G + I N + + Sbjct: 303 RLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLPS 362 Query: 367 IRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPE 426 ++ +D + + +R+K T IG LSGGNQQKV++GR + P+ Sbjct: 363 LKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPK 422 Query: 427 ILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSG 486 +L++DEPTRGID+GAK E++Q++++LA G +++ISSE+ E++ ++DRI+V G++ Sbjct: 423 VLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVA 482 Query: 487 IVDTKTTTQNEIL 499 +D +T T+ ++ Sbjct: 483 DLDAQTATEEGLM 495 Score = 80.9 bits (198), Expect = 1e-19 Identities = 63/259 (24%), Positives = 116/259 (44%), Gaps = 10/259 (3%) Query: 10 GEYLLEMSGINKSFPGVKA---LDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKD 66 G +L++ G+ + P + A L V+ R I L G GAG++ L + +FG Sbjct: 253 GAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLARLIFGADPIA 312 Query: 67 SGTILFQGKEIDFHSAKEALENGISMV---HQELNLVLQRSVMDNMWLGRYPTK---GMF 120 +G +L K + S ++A++ GI +V ++ L S+ N+ L G + Sbjct: 313 AGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLPSLKALSALGQW 372 Query: 121 VDQDKMYRETKAIFDELDIDI-DPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSS 179 VD+ + +L I + D +G LS Q + + +A + K++I+DEPT Sbjct: 373 VDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPKVLIVDEPTRG 432 Query: 180 LTEKEVNHLFTIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMD 239 + + ++ L + G +V IS ++ E+ + D + V R+G +A T + Sbjct: 433 IDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVADLDAQTATEE 492 Query: 240 KIIAMMVGRSLNQRFPDKE 258 ++A M + PD E Sbjct: 493 GLMAYMATGTDRVAAPDME 511 Score = 61.2 bits (147), Expect = 8e-14 Identities = 47/214 (21%), Positives = 98/214 (45%), Gaps = 8/214 (3%) Query: 289 GEILGIAGLVGAKRTDIVETLFGIREKSAGTITLHGKQINNHNANEAINH-GFALVTEER 347 GE+ + G GA ++ +++ L AGT+T G+ ++ +A G A + +E Sbjct: 29 GEVHALLGENGAGKSTLIKILSAAHAADAGTVTFAGQVLDPRDAPLRRQQLGIATIYQE- 87 Query: 348 RSTGIYAYLDIGFNSLISNIRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSL 407 ++ L + N + ++GL+D SR+++D Q +++ + + + L Sbjct: 88 --FNLFPELSVAENMYLGR---EPRRLGLVDWSRLRADAQALLNDLGLPL-NPDAPVRGL 141 Query: 408 SGGNQQKVIIGRWLLTQPEILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMP 467 + QQ V I + + ++++DEPT + ++ +IA L + +I +S + Sbjct: 142 TVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAIIAGLKARSVSVIYVSHRLG 201 Query: 468 ELLGITDRILVMSNGLVSGIVDTKTTTQNEILRL 501 E+ + DR VM +G D +++RL Sbjct: 202 EVKAMCDRYTVMRDGRFVASGDVADVEVADMVRL 235 Lambda K H 0.318 0.136 0.384 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: 565 Number of extensions: 30 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: 3 Length of query: 506 Length of database: 515 Length adjustment: 35 Effective length of query: 471 Effective length of database: 480 Effective search space: 226080 Effective search space used: 226080 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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