GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natE in Pseudomonas stutzeri RCH2

Align NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)
to candidate GFF1056 Psest_1089 ABC-type branched-chain amino acid transport systems, ATPase component

Query= TCDB::Q8YT15
         (247 letters)



>FitnessBrowser__psRCH2:GFF1056
          Length = 258

 Score =  111 bits (277), Expect = 2e-29
 Identities = 74/228 (32%), Positives = 119/228 (52%), Gaps = 13/228 (5%)

Query: 28  LQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKITFKGKNIAGLKSNQIVRL 87
           +  V+ +V  G +  +IGPNGAGK+T+   +   LTP  G+I ++GKNI  +K+N+I RL
Sbjct: 22  VDSVDLKVRQGHIHALIGPNGAGKTTVFNLLTKFLTPTRGEILYRGKNITSMKANEIARL 81

Query: 88  GMCYVPQIANVFPSLSVEENLEMGA---------FIRND-SLQPLKDKIFAMFPR--LSD 135
           G+    QI+ VF  +SV EN+ +           F R++ SL+ L D++  +     L  
Sbjct: 82  GLVRSFQISAVFGHMSVLENVRVALQQKMGNSFHFWRSERSLRELDDQVMQLLAEVDLQS 141

Query: 136 RRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVFEQVKQINQEGTA 195
             +  A  L  G ++ L +   L L+P +L+LDEP+  +    V  V E V++     T 
Sbjct: 142 FAQTLAVELPYGRKRALELATTLALDPFVLLLDEPTQGMGSEDVDMVVELVRKAAANRT- 200

Query: 196 IILVEQNARKALEMADRGYVLESGRDAISGPGQELLTDPKVAELYLGA 243
           +++VE N      + DR  VL  G     G  + +  +P+V E YLG+
Sbjct: 201 VLMVEHNLSVVSRLCDRITVLARGSVLAEGDYESVSANPQVREAYLGS 248


Lambda     K      H
   0.317    0.136    0.377 

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: 140
Number of extensions: 8
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: 247
Length of database: 258
Length adjustment: 24
Effective length of query: 223
Effective length of database: 234
Effective search space:    52182
Effective search space used:    52182
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 (21.6 bits)
S2: 46 (22.3 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