GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatP in Caulobacter crescentus NA1000

Align ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized)
to candidate CCNA_01670 CCNA_01670 sulfate transport ATP-binding protein cysA

Query= reanno::pseudo13_GW456_L13:PfGW456L13_4773
         (244 letters)



>FitnessBrowser__Caulo:CCNA_01670
          Length = 339

 Score =  138 bits (348), Expect = 1e-37
 Identities = 82/218 (37%), Positives = 127/218 (58%), Gaps = 10/218 (4%)

Query: 2   ISIKSINKWYGDFQVLTDCSTEVKKGEVIVVCGPSGSGKSTLIKCVNALEPFQKGDIVVD 61
           I+I+S+ K +G +  L     E+  GE++ + GPSGSGK+TL++ +  LE    G ++ D
Sbjct: 3   IAIRSVEKQFGRYPALNKVDLEIADGELLALLGPSGSGKTTLLRTIAGLEFPDAGQVLFD 62

Query: 62  GTSIADPKTNLPKLRSRVGMVFQHFELFPHLTITENLTIAQIKVLGR---SKEEATKKGL 118
           G  +    T       RVG VFQ + LF H+T+ +N+        G+   SK E  ++  
Sbjct: 63  GQDV----TYASAAARRVGFVFQQYALFKHMTVAKNIAFGLDVRKGKDKPSKAEIARRVE 118

Query: 119 QLLERVGLSAHAHKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPEMVNEVLDV 178
           +LL+ V L     ++P QLSGGQ+QRVA++RALA+ P V+L DEP  ALD   V + L  
Sbjct: 119 ELLKLVELEGLGGRYPSQLSGGQRQRVALSRALAVQPSVLLLDEPFGALD-ATVRKSLRR 177

Query: 179 MVQLAHE--GMTMMCVTHEMGFARKVADRVIFMDQGKI 214
            ++  H+  G+T + VTH+   A ++ADRV  ++ G+I
Sbjct: 178 ELRRVHDATGVTTIFVTHDQEEALELADRVAILNNGRI 215


Lambda     K      H
   0.321    0.136    0.394 

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: 179
Number of extensions: 14
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: 244
Length of database: 339
Length adjustment: 26
Effective length of query: 218
Effective length of database: 313
Effective search space:    68234
Effective search space used:    68234
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: 47 (22.7 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