GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Sinorhizobium meliloti 1021

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.

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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