Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate HSERO_RS05250 HSERO_RS05250 D-ribose transporter ATP binding protein
Query= TCDB::P0AAG8 (506 letters) >FitnessBrowser__HerbieS:HSERO_RS05250 Length = 520 Score = 439 bits (1128), Expect = e-127 Identities = 228/504 (45%), Positives = 340/504 (67%), Gaps = 8/504 (1%) Query: 4 STTPSSGEYLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIY 63 + + SS ++ + + K FPGV ALDN ++ +HALMGENGAGKSTL+K L G+Y Sbjct: 13 AASSSSSVPVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVY 72 Query: 64 QKDSGTILFQGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTK--GMFV 121 Q+DSG IL GK ++ ++A GI ++HQELNL+ S N+++GR P K G+F+ Sbjct: 73 QRDSGDILLDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFI 132 Query: 122 DQDKMYRETKAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLT 181 D+D++ R+ AIF + +D+DP VG L+V++ QM+EIAKA S++++++IMDEPT++L Sbjct: 133 DEDELNRQAAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALN 192 Query: 182 EKEVNHLFTIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKI 241 E+ LF IIR L+ +G GIVYISHKM+E+ Q+ D V+V+RDG++IAT P+ +MD I Sbjct: 193 NAEIAELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTI 252 Query: 242 IAMMVGRSLN--QRFPDKENKPGEVILEVRNLTSLRQPSIRDVSFDLHKGEILGIAGLVG 299 I+MMVGR+L+ QR P ++ +V+LEVR L R +IRDVSF L KGEILG AGL+G Sbjct: 253 ISMMVGRALDGEQRIPPDTSR-NDVVLEVRGLN--RGRAIRDVSFTLRKGEILGFAGLMG 309 Query: 300 AKRTDIVETLFGIREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIG 359 A RT++ +FG AG I +HG + + +A+ HG ++E+R+ G+ +D+ Sbjct: 310 AGRTEVARAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQ 369 Query: 360 FNSLISNIRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGR 419 N +S++ + +VG +D ++ Q + + +KTP Q LSGGNQQK++I + Sbjct: 370 ANIALSSMGRF-TRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAK 428 Query: 420 WLLTQPEILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVM 479 WLL +IL DEPTRGIDVGAK EIY+L+ LA++GK I++ISSE+PE+L ++ R+LVM Sbjct: 429 WLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVM 488 Query: 480 SNGLVSGIVDTKTTTQNEILRLAS 503 G ++G + TQ +I++LA+ Sbjct: 489 CEGRITGELARADATQEKIMQLAT 512 Score = 79.0 bits (193), Expect = 4e-19 Identities = 64/250 (25%), Positives = 120/250 (48%), Gaps = 16/250 (6%) Query: 8 SSGEYLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDS 67 S + +LE+ G+N+ +A+ +V+ +R I G GAG++ + + +FG ++ Sbjct: 272 SRNDVVLEVRGLNRG----RAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEA 327 Query: 68 GTILFQGKEIDFHSAKEALENGISMVHQE---LNLVLQRSVMDNMWL---GRYPTKGMFV 121 G I+ G + S +A+ +GI + ++ L + V N+ L GR+ G F+ Sbjct: 328 GEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTRVG-FM 386 Query: 122 DQDKMYRETKAIFDELDI---DIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTS 178 DQ + + +L I ++ +AR+ LS Q I IAK + I+ DEPT Sbjct: 387 DQRAIREAAQMYVRQLAIKTPSVEQQARL--LSGGNQQKIVIAKWLLRDCDILFFDEPTR 444 Query: 179 SLTEKEVNHLFTIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTM 238 + + ++ ++ L E+G IV IS ++ E+ ++ V V+ +G+ A T Sbjct: 445 GIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARADATQ 504 Query: 239 DKIIAMMVGR 248 +KI+ + R Sbjct: 505 EKIMQLATQR 514 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: 607 Number of extensions: 27 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: 506 Length of database: 520 Length adjustment: 35 Effective length of query: 471 Effective length of database: 485 Effective search space: 228435 Effective search space used: 228435 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