Aligments for a candidate for mglA in Shewanella sp. ANA-3

GapMind for catabolism of small carbon sources

Aligments for a candidate for mglA in Shewanella sp. ANA-3

Align Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 (characterized)
to candidate 7024900 Shewana3_2074 ABC transporter related (RefSeq)

Query= SwissProt::P23924
         (506 letters)



>FitnessBrowser__ANA3:7024900
          Length = 499

 Score =  345 bits (885), Expect = 2e-99
 Identities = 187/474 (39%), Positives = 300/474 (63%), Gaps = 11/474 (2%)

Query: 13  LLEMRGINKSFPGVKALDNVNLNVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGSIVF 72
           +LE++ I+K +PGVKAL++V+L +    +HAL+GENGAGKSTL+K + G   KD G I+F
Sbjct: 4   ILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILF 63

Query: 73  QGKEVDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKMYQDTKA 132
            G+   F++  +A + GIS V+QE+NLV   +V  N++LG  P +   +   KMY D +A
Sbjct: 64  LGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYADARA 123

Query: 133 IFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTII 192
           +  +  +DID  A +   S++  Q+I IA+  + +AK++++DEPT+SL  KEV  LF I+
Sbjct: 124 VLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGIL 183

Query: 193 RKLKERGCGIVYISHKMEEIFQLCDEITILRDGQWIATQPLEGLDMDKIIAMMVGRSLNQ 252
            +LK +G  IV+I+H +++++Q+ D IT+LR+GQ+I       L   K+I  M+GRSL +
Sbjct: 184 NQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRSLQE 243

Query: 253 RFPDKENKPGDVILEVRHLTSLR----QPSIRDVSFDLHKGEILGIAGLVGAKRTDIVET 308
           +  DK+ K   V      L SL     + SI+ ++  + KG+ +G+AGL+G+ R+++   
Sbjct: 244 QLVDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEVCNA 303

Query: 309 LFGIREKSSGTITLHGKKINNHTANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIR 368
           +FG+    SG+I L G+K+N     +AI+ G AL  E+R+  GI   L I  N +++   
Sbjct: 304 VFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIILA--- 360

Query: 369 NYKNKVG---LLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQP 425
             + ++G    L N+R +   Q+ ID +++ TP     I  LSGGNQQKVI+ RWL  +P
Sbjct: 361 -LQARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEP 419

Query: 426 EILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVM 479
            +L+LDEPTRGID+GA  EI +LI  L  +G  +++ SSE+ EL+  +++++V+
Sbjct: 420 ILLVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVL 473



 Score = 73.2 bits (178), Expect = 2e-17
 Identities = 59/239 (24%), Positives = 113/239 (47%), Gaps = 11/239 (4%)

Query: 264 VILEVRHLTSLRQPSIR---DVSFDLHKGEILGIAGLVGAKRTDIVETLFGIREKSSGTI 320
           +ILE++ + S   P ++   DVS  L  GE+  + G  GA ++ +V+ + G + K  G I
Sbjct: 3   LILELKQI-SKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDI 61

Query: 321 TLHGKKINNHTANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRNYKNKVGLLDNS 380
              G+  + +T  +A   G + V +E     +   L +  N  +        ++GL+   
Sbjct: 62  LFLGEPQHFNTPMDAQKAGISTVYQE---VNLVPNLTVAQNLFLGY---EPRRLGLIHFK 115

Query: 381 RMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILMLDEPTRGIDVG 440
           +M +D + V+   ++        +   S   QQ + I R +    ++L+LDEPT  +D  
Sbjct: 116 KMYADARAVLTQFKLDIDVS-APLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAK 174

Query: 441 AKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVDTKTTTQNEIL 499
               ++ ++ +L  KG  I+ I+  + ++  I+DRI V+ NG   G   T    Q +++
Sbjct: 175 EVQVLFGILNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLI 233



 Score = 63.9 bits (154), Expect = 1e-14
 Identities = 47/217 (21%), Positives = 103/217 (47%), Gaps = 8/217 (3%)

Query: 28  ALDNVNLNVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGSIVFQGKEVDFHSAKEALE 87
           ++ ++NL V       L G  G+G+S +   +FG+   DSGSI   G++++     +A+ 
Sbjct: 273 SIQSMNLTVPKGQAVGLAGLLGSGRSEVCNAVFGLDLVDSGSIHLAGQKLNLSQPVDAIS 332

Query: 88  NGISMVHQELNL---VLQRSVMDNMWLGRYPTKGM--FVDQDKMYQDTKAIFDELDIDI- 141
            GI++  ++  +   +   S+ +N+ L      G   ++   +  +  +   D+L I   
Sbjct: 333 AGIALCPEDRKIDGIIGPLSIRENIILALQARIGWWRYLSNTRQQEIAQFFIDKLQIATP 392

Query: 142 DPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTIIRKLKERGCG 201
           D    +  LS    Q + +A+  +    ++++DEPT  +       +  +IR L + G  
Sbjct: 393 DADKPIEQLSGGNQQKVILARWLAIEPILLVLDEPTRGIDIGAHAEIVKLIRTLCDEGMS 452

Query: 202 IVYISHKMEEIFQLCDEITILRDGQWIATQPLEGLDM 238
           ++  S +++E+    +++ +LRD    A + L G ++
Sbjct: 453 LLVASSELDELVAFSNKVVVLRDR--YAVRELSGAEL 487


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: 555
Number of extensions: 23
Number of successful extensions: 7
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: 499
Length adjustment: 34
Effective length of query: 472
Effective length of database: 465
Effective search space:   219480
Effective search space used:   219480
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, 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