Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate GFF2651 PGA1_c26910 ABC transporter, ATP-binding protein
Query= TCDB::P0AAG8 (506 letters) >FitnessBrowser__Phaeo:GFF2651 Length = 522 Score = 289 bits (739), Expect = 2e-82 Identities = 163/478 (34%), Positives = 271/478 (56%), Gaps = 8/478 (1%) Query: 13 LLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTILF 72 +L + I K F V A D+V+ + P + AL+GENGAGK+TL+ LFG Y D+G + Sbjct: 15 VLRLQNITKRFGSVTANDDVSFDLFPGEVIALLGENGAGKTTLMNILFGQYMADTGGVEL 74 Query: 73 QGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKMYRETKA 132 G + + + AL+ G+ MVHQ L +V +N+ LG P G+ + +A Sbjct: 75 FGAPLPPGAPRAALDGGVGMVHQHFTLADNLTVWENITLGVEPLLGLGLRAGPAKARIRA 134 Query: 133 IFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTII 192 + ++ + +DP A+V L+V + Q +EI KA +A+I+I+DEPT+ LT +E + LF + Sbjct: 135 LAEQFHLKVDPNAKVSRLTVGERQRVEILKALYRDARILILDEPTAVLTPQESDALFATL 194 Query: 193 RKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRSLNQ 252 R+ RG +++ISHK+ E+ + D V VLR G+ +A A D + A+MVG + Sbjct: 195 REAINRGLSVIFISHKLHEVMAISDRVLVLRHGKLVAERQTADTDSDALAALMVGADV-- 252 Query: 253 RFPDK--ENKPGEVILEVRNLTSL---RQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVE 307 P K N PG +L++R++T+ P +R VS DL G+I G+AG+ G + + + Sbjct: 253 -VPAKFAANTPGPALLQLRDVTTPSAGASPGLRHVSLDLAAGQITGLAGVSGNGQAALSD 311 Query: 308 TLFGIREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNI 367 + G+ +G++TL+G + EAI G A + E+R TG A D+ N+++ Sbjct: 312 LVSGLITPQSGSLTLNGAAPAGWSPREAITAGIARIPEDRHKTGTIADFDLTENAILETY 371 Query: 368 RNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEI 427 + G LD + + VI V+ PG T+I LSGGN QK+I+GR L P+I Sbjct: 372 ATRFSHRGWLDWRAARDFAKTVITGYDVRCPGPDTRIRLLSGGNMQKLILGRVLEQSPQI 431 Query: 428 LMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVS 485 ++ ++P RG+D+GA +++ +A+ +G +++IS ++ E++ ++D I V+S G +S Sbjct: 432 ILANQPVRGLDIGAVTYVHEQLAKACARGAAVLLISEDLDEIMQLSDVIHVISEGRLS 489 Score = 71.6 bits (174), Expect = 6e-17 Identities = 60/243 (24%), Positives = 114/243 (46%), Gaps = 17/243 (6%) Query: 265 ILEVRNLTSLRQPSIR---DVSFDLHKGEILGIAGLVGAKRTDIVETLFGIREKSAGTIT 321 +L ++N+T R S+ DVSFDL GE++ + G GA +T ++ LFG G + Sbjct: 15 VLRLQNITK-RFGSVTANDDVSFDLFPGEVIALLGENGAGKTTLMNILFGQYMADTGGVE 73 Query: 322 LHGKQINNHNANEAINHGFALVTEE---RRSTGIYAYLDIGFNSLISNIRNYKNKVGLLD 378 L G + A++ G +V + + ++ + +G L+ +GL Sbjct: 74 LFGAPLPPGAPRAALDGGVGMVHQHFTLADNLTVWENITLGVEPLLG--------LGLRA 125 Query: 379 NSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILMLDEPTRGID 438 K+ + + + +K + ++ L+ G +Q+V I + L IL+LDEPT + Sbjct: 126 GPA-KARIRALAEQFHLKVDPN-AKVSRLTVGERQRVEILKALYRDARILILDEPTAVLT 183 Query: 439 VGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVDTKTTTQNEI 498 ++ + E +G +I IS ++ E++ I+DR+LV+ +G + T T + + Sbjct: 184 PQESDALFATLREAINRGLSVIFISHKLHEVMAISDRVLVLRHGKLVAERQTADTDSDAL 243 Query: 499 LRL 501 L Sbjct: 244 AAL 246 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: 547 Number of extensions: 24 Number of successful extensions: 6 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: 522 Length adjustment: 35 Effective length of query: 471 Effective length of database: 487 Effective search space: 229377 Effective search space used: 229377 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