GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Phaeobacter inhibens BS107

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.

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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