Align Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 (characterized)
to candidate GFF2651 PGA1_c26910 ABC transporter, ATP-binding protein
Query= SwissProt::P23924 (506 letters) >FitnessBrowser__Phaeo:GFF2651 Length = 522 Score = 291 bits (744), Expect = 5e-83 Identities = 162/478 (33%), Positives = 273/478 (57%), Gaps = 8/478 (1%) Query: 13 LLEMRGINKSFPGVKALDNVNLNVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGSIVF 72 +L ++ I K F V A D+V+ ++ P + AL+GENGAGK+TL+ LFG Y D+G + Sbjct: 15 VLRLQNITKRFGSVTANDDVSFDLFPGEVIALLGENGAGKTTLMNILFGQYMADTGGVEL 74 Query: 73 QGKEVDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKMYQDTKA 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 RKLKERGCGIVYISHKMEEIFQLCDEITILRDGQWIATQPLEGLDMDKIIAMMVGRSLNQ 252 R+ RG +++ISHK+ E+ + D + +LR G+ +A + D D + A+MVG + Sbjct: 195 REAINRGLSVIFISHKLHEVMAISDRVLVLRHGKLVAERQTADTDSDALAALMVGADV-- 252 Query: 253 RFPDK--ENKPGDVILEVRHLTSL---RQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVE 307 P K N PG +L++R +T+ P +R VS DL G+I G+AG+ G + + + Sbjct: 253 -VPAKFAANTPGPALLQLRDVTTPSAGASPGLRHVSLDLAAGQITGLAGVSGNGQAALSD 311 Query: 308 TLFGIREKSSGTITLHGKKINNHTANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNI 367 + G+ SG++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 = 72.0 bits (175), Expect = 5e-17 Identities = 55/224 (24%), Positives = 105/224 (46%), Gaps = 13/224 (5%) Query: 281 DVSFDLHKGEILGIAGLVGAKRTDIVETLFGIREKSSGTITLHGKKINNHTANEAINHGF 340 DVSFDL GE++ + G GA +T ++ LFG +G + L G + A++ G Sbjct: 33 DVSFDLFPGEVIALLGENGAGKTTLMNILFGQYMADTGGVELFGAPLPPGAPRAALDGGV 92 Query: 341 ALVTEE---RRSTGIYAYLDIGFNSLISNIRNYKNKVGLLDNSRMKSDTQWVIDSMRVKT 397 +V + + ++ + +G L+ +GL K+ + + + +K Sbjct: 93 GMVHQHFTLADNLTVWENITLGVEPLLG--------LGLRAGPA-KARIRALAEQFHLKV 143 Query: 398 PGHRTQIGSLSGGNQQKVIIGRWLLTQPEILMLDEPTRGIDVGAKFEIYQLIAELAKKGK 457 + ++ L+ G +Q+V I + L IL+LDEPT + ++ + E +G Sbjct: 144 DPN-AKVSRLTVGERQRVEILKALYRDARILILDEPTAVLTPQESDALFATLREAINRGL 202 Query: 458 GIIIISSEMPELLGITDRILVMSNGLVSGIVDTKTTTQNEILRL 501 +I IS ++ E++ I+DR+LV+ +G + T T + + L Sbjct: 203 SVIFISHKLHEVMAISDRVLVLRHGKLVAERQTADTDSDALAAL 246 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: 561 Number of extensions: 26 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 ( 7.4 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