GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malI in Mariniradius saccharolyticus AK6

Align The maltose/maltooligosaccharide transporter, MalI (541 aas) (characterized)
to candidate WP_008627553.1 C943_RS21420 MFS transporter

Query= TCDB::Q9A612
         (541 letters)



>NCBI__GCF_000330725.2:WP_008627553.1
          Length = 493

 Score =  283 bits (725), Expect = 8e-81
 Identities = 168/503 (33%), Positives = 259/503 (51%), Gaps = 32/503 (6%)

Query: 39  MARQRLSFLQIWNMCFGFFGIQIGFGLQNANTSRIFQSLGVDVNHLAILWIAAPATGLLV 98
           M + +L+F QI NM  GFFGIQ  FGLQ +  + I+  LG   + + IL +A P TGLL+
Sbjct: 1   MQKPQLTFSQIINMNVGFFGIQYSFGLQQSAVNPIYDMLGAQPHEIPILNLAGPMTGLLI 60

Query: 99  QPIIGHFSDKTWG-RFGRRRPYFFWGAILTTLALLVMPNSPTLWVAAAALWIMDASINIT 157
           QPIIG  SD+TW  RFGRR+P+FF GA+  ++ L + P S TLW+AA  LW++DA+ N  
Sbjct: 61  QPIIGALSDRTWSPRFGRRKPFFFIGAVFCSICLFLYPFSSTLWMAAGLLWVLDAANNTA 120

Query: 158 MEPFRAFVGDNLPDEQRATGYAMQSFFIGLGAVFASALPWMLTNWFDVANTAPAGQVPDS 217
           MEP+RA + D LP+EQ ATG+  QSFF GLG   A+    +   +F +     AG +P  
Sbjct: 121 MEPYRALIADKLPEEQYATGFLTQSFFTGLGITLAN----LSLFFFQMYIPGTAGSLPVW 176

Query: 218 VRIAFYTGGAGLLLAVLWTVFTTREY--SPEQLTAFEKAEREIAGLGLHEEPEPSVNAYI 275
           V  +F+ G    + +V W+++ T E   SP++L   ++    +        P P +  ++
Sbjct: 177 VYASFFLGSVCSIASVGWSIYKTSEIPPSPDELQVLKEKNEGM--------PHPVIQFFL 228

Query: 276 ALGVGGVLLGAALALIVWGAGLEKELYVLAGLLFAFGLAGVAGARFKRIGRTDNGFS--- 332
           ++     +    L L+V               +F  G+        ++   +   FS   
Sbjct: 229 SVVTSLFIYALFLVLLV-------------PAIFDRGILRRTVHAIEKRPSSKVLFSQNL 275

Query: 333 EVLADVFRMPKTMRQLAVVQFFSWFGLFAMWIYTTPAVA-TVHFGAVDASSKAYNEGADW 391
           E+++ +  MP  M +LA+V  F W+ LF  W     ++A +V   +   +   Y E   W
Sbjct: 276 EIISAILDMPSVMWKLALVYLFQWYALFVYWQNAAKSIAQSVWNTSPSENMDLYEEAVGW 335

Query: 392 VGVLFAVYNGVAALAALVIPLMVKVTSRRVSHAVCLGLGALGLLSFLVIRDPGLLWIGMV 451
            G++   YN V  L+A  +  + K    +  H  CL +  LGLL F  I +  LL+  M 
Sbjct: 336 TGLVNGWYNVVTFLSAFALVGVAKRFGPKKVHFFCLIVAGLGLLVFPFIENKYLLFAPMT 395

Query: 452 GVGFAWSSILSTPYSILAGALPARKMGVYMGIFNVFIVVPQLLAATLLGLMLKTFFGNQS 511
           G G AW+S++  PY ++   +P  + GVYMGI N+ IVVP +      G + K F GN  
Sbjct: 396 GFGIAWASMMGIPYLLVVNEIPKERYGVYMGIINMMIVVPMIFQTLSFGFVAKNFLGNDP 455

Query: 512 IFALVLGALSFALAAAATFLVRD 534
             ++    +   LAA A   +++
Sbjct: 456 GISIAFAGVLLLLAAVAVLRIKE 478


Lambda     K      H
   0.327    0.140    0.437 

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: 651
Number of extensions: 38
Number of successful extensions: 4
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: 541
Length of database: 493
Length adjustment: 35
Effective length of query: 506
Effective length of database: 458
Effective search space:   231748
Effective search space used:   231748
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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