GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Methylocella silvestris BL2

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_012589117.1 MSIL_RS00330 ABC transporter ATP-binding protein

Query= uniprot:Q1MCU2
         (292 letters)



>NCBI__GCF_000021745.1:WP_012589117.1
          Length = 265

 Score =  197 bits (502), Expect = 2e-55
 Identities = 115/265 (43%), Positives = 162/265 (61%), Gaps = 10/265 (3%)

Query: 9   MSDDTLLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTM 68
           MS   LL ++ L++++GGL A+ D       G + ALIGPNGAGKT++FN I+G  +   
Sbjct: 1   MSAAPLLNIKGLTLRYGGLAAVEDLDLIVAEGALDALIGPNGAGKTSLFNLISGLTRQDD 60

Query: 69  GMITFNQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKLMKAS 128
           G I           ++RL   +  +   +ARTFQN+RLF+  T +EN+LV  H   +   
Sbjct: 61  GEIWLGGAR-----IDRLSPSQRARRG-LARTFQNLRLFTETTAIENVLVGMH---LHVG 111

Query: 129 GYTILGLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCT 188
           G  +  L   G +++    A++ AR  L    L      PAG L YG QRRLEIARA+  
Sbjct: 112 GSLLEILTRFGRFRQAERAAVDAARELLAFVGLSSVEYAPAGSLSYGDQRRLEIARALAA 171

Query: 189 GPELLCLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYG 248
            P+LL LDEPAAG+NP E+A L  LL+ +RA+   S+LL+EHDMS+VM + D + VL +G
Sbjct: 172 KPKLLLLDEPAAGMNPAETAALRLLLEKLRAQK-ISMLLVEHDMSLVMRLCDKITVLNFG 230

Query: 249 QKISDGTPDHVKNDPRVIAAYLGVE 273
           +KI++G PD V+ +P VI AYLGV+
Sbjct: 231 RKIAEGPPDAVRANPAVIEAYLGVK 255


Lambda     K      H
   0.318    0.136    0.386 

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: 211
Number of extensions: 12
Number of successful extensions: 4
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: 292
Length of database: 265
Length adjustment: 25
Effective length of query: 267
Effective length of database: 240
Effective search space:    64080
Effective search space used:    64080
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: 47 (22.7 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