Alignments for a candidate for mglA in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for mglA in Acidovorax sp. GW101-3H11

Align Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 (characterized)
to candidate Ac3H11_607 Predicted L-arabinose ABC transport system, ATP-binding protein

Query= SwissProt::P23924
         (506 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_607
          Length = 517

 Score =  307 bits (787), Expect = 5e-88
 Identities = 175/488 (35%), Positives = 274/488 (56%), Gaps = 16/488 (3%)

Query: 3   STISPPSGEYLLEMRGINKSFPGVKALDNVNLNVRPHSIHALMGENGAGKSTLLKCLFGI 62
           ST   P+   +L++ GI+K F G+  L +V LN+ P  IHALMG+NGAGKSTL+K L G+
Sbjct: 8   STAHAPAAAPVLQLSGIHKQFAGITVLRDVQLNLYPGEIHALMGQNGAGKSTLIKVLTGV 67

Query: 63  YQKDSGSIVFQGKEVDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYP----TKG 118
            +   G +   G+ V   S   A   GIS V+QE+NL    SV +N++ GRYP     +G
Sbjct: 68  LEASGGQMRLGGQAVWPDSPLAAQRLGISTVYQEVNLCPNLSVAENIFAGRYPRCGIAQG 127

Query: 119 MFVDQDKMYQDTKAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTS 178
             +D   ++Q  + +   + + ID    +    V+  Q++ IA+A S  ++++I+DEPTS
Sbjct: 128 FRIDWATLHQRARDLVARIGLQIDVTRLLSDYPVAVQQLVAIARALSIESRVLILDEPTS 187

Query: 179 SLTEKEVNHLFTIIRKLKERGCGIVYISHKMEEIFQLCDEITILRDGQWIATQPLEGLDM 238
           SL + EV  LF ++R+L+  G  IV+++H + +++ + D IT+LR+G W+     + L  
Sbjct: 188 SLDDDEVQKLFEVLRRLRSEGLSIVFVTHFLNQVYAVSDRITVLRNGSWVGEWLAKDLGP 247

Query: 239 DKIIAMMVGRSLNQRFPDKENKPGDVILEVRHLTSL------RQPSIRDVSFDLHKGEIL 292
             +IA M+GR L          P    ++ RH   L      +   ++ +   +  GE++
Sbjct: 248 QALIAAMLGRDLAAASEQPAPAPA---VDSRHANLLQAEGLGQDTQLQPLDLQIRAGEVV 304

Query: 293 GIAGLVGAKRTDIVETLFGIREKSSGTITLHGKKINNHTANEAINHGFALVTEERRSTGI 352
           G+AGL+G+ RT++   LFG+ +   G + + G+ +      +AI HG AL  EER++ GI
Sbjct: 305 GLAGLLGSGRTELARLLFGLEQPDRGALRIDGQVVKFANPMDAIRHGLALCPEERKTDGI 364

Query: 353 YAYLDIGFNSLISNIRNYKNKVG-LLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGN 411
            A L +  N  I+     +  VG  L  S      +  +  + +KT      IG LSGGN
Sbjct: 365 VAELSVREN--IALALQARMGVGKFLSRSEQTELAERYVKLLGIKTETVDKPIGLLSGGN 422

Query: 412 QQKVIIGRWLLTQPEILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLG 471
           QQK I+ RW+  +P +L+LDEPTRGIDV AK EI   I  LA+ G  ++ ISSEM E++ 
Sbjct: 423 QQKAILARWMAIEPRLLILDEPTRGIDVAAKQEIMDQILRLAQAGMAVLFISSEMSEVVR 482

Query: 472 ITDRILVM 479
           +  RI+V+
Sbjct: 483 VAHRIVVL 490



 Score = 79.7 bits (195), Expect = 2e-19
 Identities = 54/226 (23%), Positives = 111/226 (49%), Gaps = 10/226 (4%)

Query: 13  LLEMRGINKSFPGVKALDNVNLNVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGSIVF 72
           LL+  G+ +       L  ++L +R   +  L G  G+G++ L + LFG+ Q D G++  
Sbjct: 279 LLQAEGLGQD----TQLQPLDLQIRAGEVVGLAGLLGSGRTELARLLFGLEQPDRGALRI 334

Query: 73  QGKEVDFHSAKEALENGISMVHQELN---LVLQRSVMDNMWLGRYPTKGM--FVDQDKMY 127
            G+ V F +  +A+ +G+++  +E     +V + SV +N+ L      G+  F+ + +  
Sbjct: 335 DGQVVKFANPMDAIRHGLALCPEERKTDGIVAELSVRENIALALQARMGVGKFLSRSEQT 394

Query: 128 QDTKAIFDELDIDIDPRAR-VGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVN 186
           +  +     L I  +   + +G LS    Q   +A+  +   +++I+DEPT  +      
Sbjct: 395 ELAERYVKLLGIKTETVDKPIGLLSGGNQQKAILARWMAIEPRLLILDEPTRGIDVAAKQ 454

Query: 187 HLFTIIRKLKERGCGIVYISHKMEEIFQLCDEITILRDGQWIATQP 232
            +   I +L + G  +++IS +M E+ ++   I +LRD + +   P
Sbjct: 455 EIMDQILRLAQAGMAVLFISSEMSEVVRVAHRIVVLRDRRKVGELP 500



 Score = 67.4 bits (163), Expect = 1e-15
 Identities = 54/222 (24%), Positives = 99/222 (44%), Gaps = 39/222 (17%)

Query: 279 IRDVSFDLHKGEILGIAGLVGAKRTDIVETLFGIREKSSGTITLHGKKINNHTANEAINH 338
           +RDV  +L+ GEI  + G  GA ++ +++ L G+ E S G + L G+ +   +   A   
Sbjct: 34  LRDVQLNLYPGEIHALMGQNGAGKSTLIKVLTGVLEASGGQMRLGGQAVWPDSPLAAQRL 93

Query: 339 GFALVTEERR-----------------STGIYAYLDIGFNSLISNIRNYKNKVGL-LDNS 380
           G + V +E                     GI     I + +L    R+   ++GL +D +
Sbjct: 94  GISTVYQEVNLCPNLSVAENIFAGRYPRCGIAQGFRIDWATLHQRARDLVARIGLQIDVT 153

Query: 381 RMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILMLDEPTRGIDVG 440
           R+ SD    +                     QQ V I R L  +  +L+LDEPT  +D  
Sbjct: 154 RLLSDYPVAV---------------------QQLVAIARALSIESRVLILDEPTSSLDDD 192

Query: 441 AKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNG 482
              ++++++  L  +G  I+ ++  + ++  ++DRI V+ NG
Sbjct: 193 EVQKLFEVLRRLRSEGLSIVFVTHFLNQVYAVSDRITVLRNG 234


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: 573
Number of extensions: 25
Number of successful extensions: 8
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: 517
Length adjustment: 35
Effective length of query: 471
Effective length of database: 482
Effective search space:   227022
Effective search space used:   227022
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 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
the source code
instructions for running GapMind on your computer

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