GapMind for catabolism of small carbon sources

 

Aligments for a candidate for hutV in Caulobacter crescentus NA1000

Align HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate CCNA_01670 CCNA_01670 sulfate transport ATP-binding protein cysA

Query= TCDB::Q9KKE1
         (275 letters)



>lcl|FitnessBrowser__Caulo:CCNA_01670 CCNA_01670 sulfate transport
           ATP-binding protein cysA
          Length = 339

 Score =  167 bits (422), Expect = 4e-46
 Identities = 93/226 (41%), Positives = 134/226 (59%), Gaps = 10/226 (4%)

Query: 43  LNDVSLKIGAGKIFVIMGLSGSGKSTLVRHINRLIEPTSGEVLFDGDNILDLGAKALRAF 102
           LN V L+I  G++  ++G SGSGK+TL+R I  L  P +G+VLFDG ++    A A    
Sbjct: 18  LNKVDLEIADGELLALLGPSGSGKTTLLRTIAGLEFPDAGQVLFDGQDVTYASAAA---- 73

Query: 103 RMRRVSMVFQSFALMPHRTVLQNVVYGQRVR-GVSKDDAREIGMK---WIDTVGLSGYDA 158
             RRV  VFQ +AL  H TV +N+ +G  VR G  K    EI  +    +  V L G   
Sbjct: 74  --RRVGFVFQQYALFKHMTVAKNIAFGLDVRKGKDKPSKAEIARRVEELLKLVELEGLGG 131

Query: 159 KFPHQLSGGMKQRVGLARALAADTDVILMDEAFSALDPLIRGDMQDQLLQLQRNLAKTIV 218
           ++P QLSGG +QRV L+RALA    V+L+DE F ALD  +R  ++ +L ++      T +
Sbjct: 132 RYPSQLSGGQRQRVALSRALAVQPSVLLLDEPFGALDATVRKSLRRELRRVHDATGVTTI 191

Query: 219 FITHDLDEALRIGSEIAILRDGQVVQVGTPNDILDNPANDYVARFV 264
           F+THD +EAL +   +AIL +G++ Q+GTP+ + D P   +V  FV
Sbjct: 192 FVTHDQEEALELADRVAILNNGRIEQIGTPDQVHDAPETAFVCGFV 237


Lambda     K      H
   0.323    0.139    0.397 

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: 231
Number of extensions: 14
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: 275
Length of database: 339
Length adjustment: 27
Effective length of query: 248
Effective length of database: 312
Effective search space:    77376
Effective search space used:    77376
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: 48 (23.1 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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