Align Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 (characterized)
to candidate 8502321 DvMF_3029 ABC transporter related (RefSeq)
Query= SwissProt::P23924 (506 letters) >FitnessBrowser__Miya:8502321 Length = 537 Score = 271 bits (693), Expect = 4e-77 Identities = 160/490 (32%), Positives = 273/490 (55%), Gaps = 8/490 (1%) Query: 13 LLEMRGINKSFPGVKALDNVNLNVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGSIVF 72 ++ + GI KSF V+A ++ L++RP I AL+GENGAGKSTL+ L G ++D+G+IV Sbjct: 29 VVRLDGICKSFGKVRANHDITLDIRPGCIKALLGENGAGKSTLMSILAGKLRQDAGTIVV 88 Query: 73 QGKEVDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKMYQDTKA 132 G F S ++AL GI MV+Q LV +V +N+ LG+ P M + +M + A Sbjct: 89 DGVPTVFASPRDALRAGIGMVYQHFMLVDSMTVAENVLLGQSPD--MLLRPARMRDEVAA 146 Query: 133 IFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTII 192 + + + +DP ARVG LS+ + Q +EI K +++++I+DEPT+ LT +E + LF + Sbjct: 147 LAERYGLAVDPAARVGGLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPRETDQLFEAM 206 Query: 193 RKLKERGCGIVYISHKMEEIFQLCDEITILRDGQWIATQPLEGLDMDKIIA-MMVGRSLN 251 ++ ++G +V+ISHK++E+ + DEI ILR G+ + + ++A MVGR + Sbjct: 207 WRMADQGKALVFISHKLQEVLTVADEIAILRRGEVVDEFSEADVPNQTVLANRMVGRDVV 266 Query: 252 QRFPDKENKPGDVILEVRHLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVETLFG 311 + K P D +L V HL+ + DVS + +GEI+ IAG+ G + ++VE + G Sbjct: 267 LQVDAKRLTPVDTVLSVEHLSG---AGLSDVSLQVRRGEIVAIAGVAGNGQKELVEAICG 323 Query: 312 IREKSSGTITLHGKKINNHTANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRNYK 371 + +G + + G+ A G A + E+R+ +LD+ N L++ RN Sbjct: 324 LARPEAGEVRILGRPWREFFAGPPGRRGLAYIPEDRQGLATCRHLDLVDNFLLTT-RNQF 382 Query: 372 NKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILMLD 431 K LD + + + V+ V+ +LSGGN QK++IGR +PE+++ + Sbjct: 383 AKGVFLDRTEATNAVKRVVWEYNVQPGDITAPARALSGGNLQKLVIGREFFRKPEVIVAE 442 Query: 432 EPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVDTK 491 PT+G+D+ A E++ + E A+ G+++++ ++ E L + DRI VM G + D Sbjct: 443 NPTQGLDISATEEVWGRLLE-ARSTSGVLLVTGDLNEALELADRIAVMYRGRFIDVFDKD 501 Query: 492 TTTQNEILRL 501 T + + + L Sbjct: 502 DTAKVQAIGL 511 Lambda K H 0.319 0.137 0.388 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: 558 Number of extensions: 26 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 506 Length of database: 537 Length adjustment: 35 Effective length of query: 471 Effective length of database: 502 Effective search space: 236442 Effective search space used: 236442 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 (21.7 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