Aligments for a candidate for mglA in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Aligments 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)



>lcl|FitnessBrowser__Smeli:SM_b21376 SM_b21376 sugar uptake ABC
           transporter ATP-binding protein
          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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources