GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK in Phaeacidiphilus oryzae TH49

Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate WP_037572389.1 BS73_RS14235 ABC transporter ATP-binding protein

Query= reanno::psRCH2:GFF857
         (371 letters)



>NCBI__GCF_000744815.1:WP_037572389.1
          Length = 386

 Score =  221 bits (562), Expect = 3e-62
 Identities = 121/281 (43%), Positives = 168/281 (59%), Gaps = 6/281 (2%)

Query: 6   LRDICKSYDGTPITRHIDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDITSGDLLIDNQ 65
           L  + K +        +DL I  G F   +G SGCGK+T LR+I+GLE  T+G + + +Q
Sbjct: 21  LTGLTKKFGSFTAVDGVDLTIAQGSFFALLGASGCGKTTTLRMISGLEAPTAGRIHLGDQ 80

Query: 66  RVNDLPPKDRSVGMVFQSYALYPHMTVAENMAFGLKLASVDKREIKRRVEAVAEILQLDK 125
            V D  P  R V  VFQ+YAL+PH+ + EN+AFGL+   +  R +K+ VE + ++++L  
Sbjct: 81  DVTDRKPYRRPVNTVFQNYALFPHLDIFENVAFGLRRRGI--RSVKKPVEDMLDLVELGH 138

Query: 126 LLERKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAFLRVQMRIEIARLHQRIRS 185
           L  RKP  LSGGQ+QR+A+ R ++ +P+V L DEPL  LD  LR QM+IE+ R+   +  
Sbjct: 139 LARRKPTQLSGGQQQRIALARALINQPQVLLLDEPLGALDLKLRRQMQIELKRIQLEVGL 198

Query: 186 TMIYVTHDQVEAMTLADKIVVLNAGEIAQVGQPLHLYHYPKNRFVAGFLGSPQMNFVEVR 245
           T ++VTHDQ EAMT+AD I V+N G I Q+G P  LY  P   FVA FLG  Q N +   
Sbjct: 199 TFVHVTHDQEEAMTMADTIAVMNHGRIEQLGSPAELYENPNTTFVANFLG--QSNLIAGT 256

Query: 246 AISASPETVTIELPSGYPLTLPVDGSAVSPGDPLTLGIRPE 286
             S S + V +    G  L LP      + G P+ LG+RPE
Sbjct: 257 VESVSGDVVQV-AAHGRSLALPAARCRTTSG-PVILGVRPE 295


Lambda     K      H
   0.322    0.139    0.405 

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: 329
Number of extensions: 16
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: 371
Length of database: 386
Length adjustment: 30
Effective length of query: 341
Effective length of database: 356
Effective search space:   121396
Effective search space used:   121396
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 (21.9 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