Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate SM_b21376 SM_b21376 sugar uptake ABC transporter ATP-binding protein
Query= TCDB::P0AAG8 (506 letters) >FitnessBrowser__Smeli:SM_b21376 Length = 503 Score = 379 bits (972), Expect = e-109 Identities = 196/499 (39%), Positives = 322/499 (64%), Gaps = 6/499 (1%) Query: 8 SSGEYLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDS 67 S+ + +L+++ + KSF V AL + L+VR +H L+GENGAGKSTL+K L G++ S Sbjct: 4 SAADTILKITDVTKSFGQVAALKGMRLEVRRGRVHTLLGENGAGKSTLMKILAGVHGATS 63 Query: 68 GTILFQGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKMY 127 G I+ G+ + +EA G+++V QEL+L +V +N+ R P + F++ + Sbjct: 64 GEIVLDGQAYRPANPQEAASLGLAIVFQELSLCNNLTVAENILATREPRRFGFINDKALV 123 Query: 128 RETKAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNH 187 + I +L + ID +VG LS++Q Q++EIAK S++AK+VI+DEPTSSL++ E Sbjct: 124 AKAHRIVADLRLPIDVTEKVGNLSIAQRQLVEIAKGLSHDAKVVILDEPTSSLSDSEAEI 183 Query: 188 LFTIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVG 247 LF II +L++RG I+YISH+MEEI +L D++TV+RDG++++T +T++ +IA+MVG Sbjct: 184 LFEIIGRLRQRGAAIIYISHRMEEIMRLSDDITVIRDGEYVSTHARDEVTIETLIALMVG 243 Query: 248 RSLNQRFPDKENKPG---EVILEVRNLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTD 304 R +++ +P + +L V LT R+ +DVSFD+ GEILG GLVG+ R++ Sbjct: 244 RRMDEIYPPPVHHVAADRAPVLAVDRLT--REGEFQDVSFDVRAGEILGFFGLVGSGRSE 301 Query: 305 IVETLFGIREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLI 364 ++ LFG++ +AGT+ L G+ + + ++AI G VTE R+ G+ + +N + Sbjct: 302 VMNALFGMK-SAAGTVRLDGEVVRFRSPDQAIARGVGFVTENRKEEGLVLGHSVEWNISM 360 Query: 365 SNIRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQ 424 + + ++ +G + N ++ + + +KT T G+LSGGNQQK+++ +WLLT+ Sbjct: 361 AALADFAGGLGFIRNGAERAAASEQVGKLSIKTNSLETPAGALSGGNQQKIVLAKWLLTR 420 Query: 425 PEILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLV 484 P++L+LDEPTRG+DVGAKFEIY++I ELA +G I++ISS++PE+LG++DR++VM G Sbjct: 421 PKVLILDEPTRGVDVGAKFEIYKIIRELAAEGTAILLISSDLPEVLGMSDRVVVMHEGAP 480 Query: 485 SGIVDTKTTTQNEILRLAS 503 ++ T I+ A+ Sbjct: 481 GATLEGSALTPETIMAHAT 499 Score = 74.7 bits (182), Expect = 7e-18 Identities = 63/224 (28%), Positives = 102/224 (45%), Gaps = 8/224 (3%) Query: 31 NVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTILFQGKEIDFHSAKEALENGI 90 +V+ VR I G G+G+S ++ LFG+ + +GT+ G+ + F S +A+ G+ Sbjct: 278 DVSFDVRAGEILGFFGLVGSGRSEVMNALFGM-KSAAGTVRLDGEVVRFRSPDQAIARGV 336 Query: 91 SMV---HQELNLVLQRSVMDNMWLGRYP--TKGM-FVDQDKMYRETKAIFDELDIDIDP- 143 V +E LVL SV N+ + G+ F+ +L I + Sbjct: 337 GFVTENRKEEGLVLGHSVEWNISMAALADFAGGLGFIRNGAERAAASEQVGKLSIKTNSL 396 Query: 144 RARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTIIRKLKERGCGIV 203 G LS Q I +AK K++I+DEPT + ++ IIR+L G I+ Sbjct: 397 ETPAGALSGGNQQKIVLAKWLLTRPKVLILDEPTRGVDVGAKFEIYKIIRELAAEGTAIL 456 Query: 204 YISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVG 247 IS + E+ + D V V+ +G AT + LT + I+A G Sbjct: 457 LISSDLPEVLGMSDRVVVMHEGAPGATLEGSALTPETIMAHATG 500 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: 574 Number of extensions: 23 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: 503 Length adjustment: 34 Effective length of query: 472 Effective length of database: 469 Effective search space: 221368 Effective search space used: 221368 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