Align Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 (characterized)
to candidate WP_085124759.1 B9O00_RS21320 sugar ABC transporter ATP-binding protein
Query= SwissProt::P23924 (506 letters) >NCBI__GCF_900177295.1:WP_085124759.1 Length = 518 Score = 318 bits (814), Expect = 4e-91 Identities = 169/488 (34%), Positives = 285/488 (58%), Gaps = 2/488 (0%) Query: 13 LLEMRGINKSFPGVKALDNVNLNVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGSIVF 72 LLE+RG+++ FPGV ALD V+ +RP +H L GENGAGKST++ + G + G F Sbjct: 23 LLELRGVSRRFPGVLALDKVDFQLRPGEVHVLFGENGAGKSTMISMIAGALRPSEGEFRF 82 Query: 73 QGKEVDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKMYQDTKA 132 +G+ V+ +S A GIS V QE +LV Q +V +N++LG T+ +D+ ++ A Sbjct: 83 RGEPVELNSVHHARGLGISAVFQEFSLVPQMTVEENLFLGAESTRLGLLDRRALHDRADA 142 Query: 133 IFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTII 192 I L + PR RV L+ ++ QM+EIAKAF ++I+DEPT+SLTE+E LF +I Sbjct: 143 ILKRLGFPLRPRDRVLHLTRAEQQMVEIAKAFRSELSVLILDEPTASLTERETAQLFKLI 202 Query: 193 RKLKERGCGIVYISHKMEEIFQLCDEITILRDGQWIATQPLEGLDMDKIIAMMVGRSLNQ 252 ++K +G G++YI+H++ EI ++ D IT+LRDG+++AT + +++ +M GR ++ Sbjct: 203 EQVKAQGVGVIYITHRLSEIRRIGDRITVLRDGRYVATVDAQTTPEGELVRLMTGRVYDE 262 Query: 253 RFPDKENKPGDVILEVRHLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVETLFGI 312 FP KPG +L V LT+ S+ + S + GEI+G+AGLVG+ ++++ FG+ Sbjct: 263 LFPKVRFKPGRELLSVERLTT-ASGSVVEASLSVCAGEIVGLAGLVGSGKSEVARACFGL 321 Query: 313 REKSSGTITLHGKKINNHTANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRNYKN 372 + + G + L G+++ + GF V +RR G+ + N + ++ Sbjct: 322 EKIAEGHVRLKGEEVTGQGPKRMLKRGFFYVPPDRRDEGLMMMRPVRENVSLPSLTLAPF 381 Query: 373 KVGLLDNSRMKSD-TQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILMLD 431 G L + R ++D + + + + ++ P + + SGGNQQKV++ + ++ D Sbjct: 382 GNGALLDRRGETDRVRRLAEQLNLQPPRIERAVEAFSGGNQQKVLLAKSRTRPVQVFAFD 441 Query: 432 EPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVDTK 491 EPT G+DVG + IY+ I +L + G GI++ISS++PE+L +++R V G V + Sbjct: 442 EPTVGVDVGTRVAIYEFIRDLCEAGAGILLISSDLPEVLNLSNRAYVFYRGRVQAELAGD 501 Query: 492 TTTQNEIL 499 T+ ++L Sbjct: 502 EITEEKVL 509 Score = 76.6 bits (187), Expect = 2e-18 Identities = 60/244 (24%), Positives = 114/244 (46%), Gaps = 11/244 (4%) Query: 261 PGDVILEVRHLTSLRQPSIR---DVSFDLHKGEILGIAGLVGAKRTDIVETLFGIREKSS 317 P +LE+R + S R P + V F L GE+ + G GA ++ ++ + G S Sbjct: 19 PAAPLLELRGV-SRRFPGVLALDKVDFQLRPGEVHVLFGENGAGKSTMISMIAGALRPSE 77 Query: 318 GTITLHGKKINNHTANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRNYKNKVGLL 377 G G+ + ++ + A G + V +E + + + N + ++GLL Sbjct: 78 GEFRFRGEPVELNSVHHARGLGISAVFQE---FSLVPQMTVEENLFLGA---ESTRLGLL 131 Query: 378 DNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILMLDEPTRGI 437 D + ++ + R ++ L+ QQ V I + ++ +L+LDEPT + Sbjct: 132 DRRALHDRADAILKRLGFPLRP-RDRVLHLTRAEQQMVEIAKAFRSELSVLILDEPTASL 190 Query: 438 DVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVDTKTTTQNE 497 ++++LI ++ +G G+I I+ + E+ I DRI V+ +G VD +TT + E Sbjct: 191 TERETAQLFKLIEQVKAQGVGVIYITHRLSEIRRIGDRITVLRDGRYVATVDAQTTPEGE 250 Query: 498 ILRL 501 ++RL Sbjct: 251 LVRL 254 Score = 58.5 bits (140), Expect = 5e-13 Identities = 52/220 (23%), Positives = 98/220 (44%), Gaps = 10/220 (4%) Query: 33 NLNVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGSIVFQGKEVDFHSAKEALENGISM 92 +L+V I L G G+GKS + + FG+ + G + +G+EV K L+ G Sbjct: 292 SLSVCAGEIVGLAGLVGSGKSEVARACFGLEKIAEGHVRLKGEEVTGQGPKRMLKRGFFY 351 Query: 93 V---HQELNLVLQRSVMDNMWLGRYPT----KGMFVDQDKMYQDTKAIFDELDIDIDPRA 145 V ++ L++ R V +N+ L G +D+ + + ++L++ PR Sbjct: 352 VPPDRRDEGLMMMRPVRENVSLPSLTLAPFGNGALLDRRGETDRVRRLAEQLNLQ-PPRI 410 Query: 146 R--VGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTIIRKLKERGCGIV 203 V S Q + +AK+ + ++ DEPT + ++ IR L E G GI+ Sbjct: 411 ERAVEAFSGGNQQKVLLAKSRTRPVQVFAFDEPTVGVDVGTRVAIYEFIRDLCEAGAGIL 470 Query: 204 YISHKMEEIFQLCDEITILRDGQWIATQPLEGLDMDKIIA 243 IS + E+ L + + G+ A + + +K+++ Sbjct: 471 LISSDLPEVLNLSNRAYVFYRGRVQAELAGDEITEEKVLS 510 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: 518 Number of extensions: 18 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 506 Length of database: 518 Length adjustment: 35 Effective length of query: 471 Effective length of database: 483 Effective search space: 227493 Effective search space used: 227493 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 Apr 09 2024. 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