GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Alkalihalobacterium alkalinitrilicum DSM 22532

Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate WP_078427103.1 BK574_RS00955 ABC transporter ATP-binding protein

Query= TCDB::P0AAG8
         (506 letters)



>NCBI__GCF_002019605.1:WP_078427103.1
          Length = 509

 Score =  334 bits (857), Expect = 4e-96
 Identities = 179/491 (36%), Positives = 288/491 (58%), Gaps = 4/491 (0%)

Query: 12  YLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTIL 71
           Y++EM  I K FPG+ A DNV L+V+   IHAL+GENGAGKSTL+  LFG+YQ + G IL
Sbjct: 3   YVIEMKDIRKEFPGIVANDNVTLQVKQGEIHALLGENGAGKSTLMNVLFGLYQPEKGEIL 62

Query: 72  FQGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKMYRETK 131
            +GK +       A   GI MVHQ   LV + +V +N+ LG+ PT G  ++  K  +  +
Sbjct: 63  VKGKPVKITDPNVANRLGIGMVHQHFMLVEKFTVTENIILGKEPTAGGKINIKKAAKAVE 122

Query: 132 AIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTI 191
            I  +  + +DP A++  +SV   Q +EI K     A+I+I DEPT++LT +E+  L  I
Sbjct: 123 TISKQYGLAVDPYAKIQDISVGMQQRVEILKTLYRGAEILIFDEPTAALTPQEITELIQI 182

Query: 192 IRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRSLN 251
           ++KL   G  I+ I+HK++EI ++CD  TV+R G+ I T  ++  T D + AMMVGR +N
Sbjct: 183 MKKLVSEGKSIILITHKLKEIMEVCDRCTVIRRGRGIGTVDISESTPDSLAAMMVGREVN 242

Query: 252 QRFPDKENKPGEVILEVRNLT---SLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVET 308
                   +P + +L++++L    S    ++ D+  ++H GEILG+AG+ G  +T+++E 
Sbjct: 243 FSVEKDPAQPKDAVLQIKDLVVKDSRDITAVNDLHLEVHAGEILGVAGVDGNGQTELIEA 302

Query: 309 LFGIREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLISN-I 367
           + G+R+ + G I L+G+ I      +    G   + ++R   G+     +G N ++    
Sbjct: 303 ITGLRKPTGGNIQLNGQDITGLTPRKITGAGVGHIPQDRHKHGLVLDFTVGENIVLQTYY 362

Query: 368 RNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEI 427
           +   +  G+L+ + +      +I+   V+TP   T   +LSGGNQQK II R +   P++
Sbjct: 363 QKPYSTSGVLNFNEIYKKANELIEDYDVRTPSEHTLARALSGGNQQKAIIAREVDRSPDL 422

Query: 428 LMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGI 487
           L+  +PTRG+DVGA   I+  + +   KGK +++IS E+ E+L ++DRI V+  G +  I
Sbjct: 423 LIAAQPTRGLDVGAIESIHHRLVKERDKGKAVLLISLELDEVLNVSDRIAVIYEGKIVAI 482

Query: 488 VDTKTTTQNEI 498
           VD   T +NE+
Sbjct: 483 VDADKTNENEL 493


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: 596
Number of extensions: 26
Number of successful extensions: 5
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: 509
Length adjustment: 34
Effective length of query: 472
Effective length of database: 475
Effective search space:   224200
Effective search space used:   224200
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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