GapMind for catabolism of small carbon sources

 

Aligments for a candidate for proV in Caulobacter crescentus NA1000

Align Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized)
to candidate CCNA_01670 CCNA_01670 sulfate transport ATP-binding protein cysA

Query= SwissProt::P17328
         (400 letters)



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

 Score =  166 bits (421), Expect = 7e-46
 Identities = 93/248 (37%), Positives = 140/248 (56%), Gaps = 19/248 (7%)

Query: 21  AFKYIEKGLSKEQILEKTGLSLGVKDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEP 80
           A + +EK   +   L K  L          I +GE+  ++G SGSGK+T++R +  L  P
Sbjct: 4   AIRSVEKQFGRYPALNKVDLE---------IADGELLALLGPSGSGKTTLLRTIAGLEFP 54

Query: 81  TRGQVLIDGVDIAKISDAELREVRRKKIAMVFQSFALMPHMTVLDNTAFGMELAG----I 136
             GQVL DG D+   S A       +++  VFQ +AL  HMTV  N AFG+++       
Sbjct: 55  DAGQVLFDGQDVTYASAAA------RRVGFVFQQYALFKHMTVAKNIAFGLDVRKGKDKP 108

Query: 137 AAQERREKALDALRQVGLENYAHAYPDELSGGMRQRVGLARALAINPDILLMDEAFSALD 196
           +  E   +  + L+ V LE     YP +LSGG RQRV L+RALA+ P +LL+DE F ALD
Sbjct: 109 SKAEIARRVEELLKLVELEGLGGRYPSQLSGGQRQRVALSRALAVQPSVLLLDEPFGALD 168

Query: 197 PLIRTEMQDELVKLQAKHQRTIVFISHDLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNP 256
             +R  ++ EL ++      T +F++HD +EA+ + DR+AI+ NG + Q+GTPD++ + P
Sbjct: 169 ATVRKSLRRELRRVHDATGVTTIFVTHDQEEALELADRVAILNNGRIEQIGTPDQVHDAP 228

Query: 257 ANDYVRTF 264
              +V  F
Sbjct: 229 ETAFVCGF 236


Lambda     K      H
   0.319    0.137    0.378 

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: 303
Number of extensions: 12
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: 400
Length of database: 339
Length adjustment: 30
Effective length of query: 370
Effective length of database: 309
Effective search space:   114330
Effective search space used:   114330
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: 49 (23.5 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