Alignments for a candidate for proB in Caulobacter crescentus NA1000

GapMind for Amino acid biosynthesis

Alignments for a candidate for proB in Caulobacter crescentus NA1000

Align Delta-1-pyrroline-5-carboxylate synthase; P5CS; Aldehyde dehydrogenase family 18 member A1; EC 2.7.2.11; EC 1.2.1.41 (characterized)
to candidate CCNA_03543 CCNA_03543 gamma-glutamyl phosphate reductase

Query= SwissProt::P54886
         (795 letters)



>FitnessBrowser__Caulo:CCNA_03543
          Length = 424

 Score =  266 bits (681), Expect = 1e-75
 Identities = 168/411 (40%), Positives = 226/411 (54%), Gaps = 19/411 (4%)

Query: 367 GEMARSGGRMLATLEPEQRAEIIHHLADLLTDQRDEILLANKKDLEEAEGR-LAAPLLKR 425
           G  AR G R L    PEQR   I  +A  + +  D IL AN KDL  AE   ++ P+L R
Sbjct: 16  GRTAREGARALRLATPEQRTAAIQAMAVAIREDADAILTANAKDLARAEANGVSGPMLDR 75

Query: 426 LSLSTSKLNSLAIGLRQIAASSQDSVGRVLRRTRIAKNLELEQVTVPIGVLLVIFESRPD 485
           L+L  ++L  +A G+  +AA   D VG    R      L++ +V  PIGV+ +I+ESRP+
Sbjct: 76  LALDAARLEGVAAGVEAVAAVP-DPVGVATSRWTRPNGLDIARVRTPIGVIAMIYESRPN 134

Query: 486 CLPQVAALAIASGNGLLLKGGKEAAHSNRILHLLTQEALSIHGVKEA-VQLVNTREEVED 544
                AAL + SGN ++L+GG E  HSN  +H      L   G+  A VQ V T +    
Sbjct: 135 VTADAAALCVRSGNAVILRGGSECIHSNLAIHAAIARGLQKAGLPTAAVQAVKTPDRAAV 194

Query: 545 ---LCRLDKMIDLIIPRGSSQLVRDIQKAAKGIPVMGHSEGICHMYVDSEASVDKVTRLV 601
              L  LD+ IDLIIPRG   LV  +Q  A+  PV+GH EG+ H++V + A + K   +V
Sbjct: 195 GMILAGLDRTIDLIIPRGGKSLVARVQAEARA-PVLGHLEGLNHVFVHAAADLKKAVEVV 253

Query: 602 RDSKCEYPAACNALETLLIHR---DLLRTPLFDQIIDM---LRVEQVKIHAGPKFASYLT 655
            ++K    + C + ETLLI +   D L  P+ D +I     LR +       P      T
Sbjct: 254 VNAKLRRVSVCGSAETLLIDQAAADKLLPPIADALIKAGCELRGDAAARAIEP------T 307

Query: 656 FSPSEVKSLRTEYGDLELCIEVVDNVQDAIDHIHKYGSSHTDVIVTEDENTAEFFLQHVD 715
              + V+   TEY    L + VVD V  A  HI  YGS HTD I+TED   AE F+  VD
Sbjct: 308 MKKATVEDWTTEYLAPILSVAVVDGVAGAARHIASYGSGHTDAIITEDAAAAEAFIAEVD 367

Query: 716 SACVFWNASTRFSDGYRFGLGAEVGISTSRIHARGPVGLEGLLTTKWLLRG 766
           SA V  NAST+F+DG  FG GAE+GI+T ++HARGPVG E L T K+++RG
Sbjct: 368 SAIVLVNASTQFADGGEFGFGAEIGIATDKLHARGPVGAEQLTTFKYVVRG 418


Lambda     K      H
   0.319    0.135    0.387 

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: 692
Number of extensions: 25
Number of successful extensions: 6
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: 795
Length of database: 424
Length adjustment: 36
Effective length of query: 759
Effective length of database: 388
Effective search space:   294492
Effective search space used:   294492
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: 53 (25.0 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis