GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Aa in Phaeacidiphilus oryzae TH49

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_037573817.1 BS73_RS18100 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= BRENDA::Q70HW1
         (384 letters)



>NCBI__GCF_000744815.1:WP_037573817.1
          Length = 369

 Score =  360 bits (925), Expect = e-104
 Identities = 198/369 (53%), Positives = 245/369 (66%), Gaps = 10/369 (2%)

Query: 1   MARVLLEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEG 60
           MA V  +   + YPG  +P V   +L+I D EF V VGPSGCGK+T+LRM+AGLED+  G
Sbjct: 1   MATVTYDKATRIYPGGDKPAVDALDLEIADGEFLVLVGPSGCGKSTSLRMLAGLEDVNNG 60

Query: 61  NLYIGDRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAA 120
            + IG+R V  +PPKDRDIAMVFQNYALYPHMTV  NM F LK+  V KAEI  +V+EAA
Sbjct: 61  AIRIGERDVTHLPPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVNKAEIRSKVEEAA 120

Query: 121 KILDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRK 180
           KILD+   LDRKPKALSGGQRQRVA+GRAIVREPQVFLMDEPLSNLDAKLRV  R +I  
Sbjct: 121 KILDLTEFLDRKPKALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIAG 180

Query: 181 LHQRLQTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPA 240
           L +RL  T +YVTHDQ EAMTMGDR+ V++DG++QQ DTP+ +Y +P N+FVAGFIGSPA
Sbjct: 181 LQRRLGITTVYVTHDQVEAMTMGDRVAVLKDGLLQQVDTPRNMYDRPANLFVAGFIGSPA 240

Query: 241 MNFIRGEIVQDGDAFYFRAPSISLRLPEGRYGVLKASGAIGKPVVLGVRPEDLHDEEVFM 300
           MN +   I   G  F      +S      R  V +A+ A  K V +GVRPE L       
Sbjct: 241 MNLVEVPITDGGVKFGESVVQVS------RDAVGEAANAGDKTVTVGVRPEHLDIVGGTE 294

Query: 301 TTYPDSVLQMQVEVVEHMGSEVYLHTS--IGPNTI--VARVNPRHVYHVGSSVKLAIDLN 356
               D  L + V VVE +G++ Y++ S  +G  TI  V RV  R +   G  +++     
Sbjct: 295 GGGEDKGLAVTVNVVEELGADGYVYGSAKVGTETIDLVVRVGGRDIPMKGDQLRVVPRAG 354

Query: 357 KIHIFDAET 365
           + H+F   T
Sbjct: 355 ETHVFSTST 363


Lambda     K      H
   0.321    0.138    0.395 

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: 453
Number of extensions: 15
Number of successful extensions: 2
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: 384
Length of database: 369
Length adjustment: 30
Effective length of query: 354
Effective length of database: 339
Effective search space:   120006
Effective search space used:   120006
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 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. 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