GapMind for catabolism of small carbon sources

 

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

Align MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized)
to candidate Ac3H11_2066 SN-glycerol-3-phosphate transport ATP-binding protein UgpC (TC 3.A.1.1.3)

Query= TCDB::Q8DT25
         (377 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2066
          Length = 355

 Score =  283 bits (725), Expect = 4e-81
 Identities = 164/378 (43%), Positives = 225/378 (59%), Gaps = 30/378 (7%)

Query: 2   TTLKLDNIYKRYPNAKHYSVENFNLDIH--DKEFIVFVGPSGCGKSTTLRMIAGLEDITE 59
           ++L +  I KR+            +DIH    EF++ VGPSGCGKST L +IAGL++ TE
Sbjct: 3   SSLDIAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTE 62

Query: 60  GNLYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEA 119
           G + I  K +    P+DRDIAMVFQ+YALYP +SV +N+ F L++RK  K +  KR+ E 
Sbjct: 63  GEIRIGGKNVVGMPPRDRDIAMVFQSYALYPTLSVADNIGFALEMRKMPKPERQKRIDEV 122

Query: 120 AEILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIA 179
           A +L ++  L+R+P+ LSGGQRQRVAMGRA+ R  ++FL DEPLSNLDAKLRV MRAEI 
Sbjct: 123 AAMLQISHLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMRAEIK 182

Query: 180 KIHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPAN 239
           ++H+  G T++YVTHDQ EAMTL  RI +M            G ++Q+GTP E+YN PAN
Sbjct: 183 RLHQASGITSVYVTHDQVEAMTLGSRIAVMKG----------GVVQQLGTPDEIYNRPAN 232

Query: 240 KFVAGFIGSPAMNFFEVTVEKERL-VNQDGLSLALPQGQEKILEEKGYLGKKVTLGIRPE 298
            +VA FIGSP MN     V   +  +    L+LA P               +V LG+RPE
Sbjct: 233 TYVATFIGSPTMNLLRGAVTGGQFGIQGAALNLAPPPSS----------ANEVLLGVRPE 282

Query: 299 DISSDQIVHETFPNASVTADILVSELLGSESMLYVKFGSTEFTARVNARDSHSPGEKVQL 358
            +    ++ ET P       + V E  G ++ + V   +   T R +A+    PGE V L
Sbjct: 283 HL----VMQETAP---WRGRVSVVEPTGPDTYVMVDTAAGSVTLRTDAQTRVQPGEHVGL 335

Query: 359 TFNIAKGHFFDLETEKRI 376
               A  H+FD ++E+R+
Sbjct: 336 ALAPAHAHWFDAQSEERL 353


Lambda     K      H
   0.318    0.135    0.379 

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: 324
Number of extensions: 19
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 377
Length of database: 355
Length adjustment: 30
Effective length of query: 347
Effective length of database: 325
Effective search space:   112775
Effective search space used:   112775
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: 49 (23.5 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