Alignments for a candidate for ams in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Alignments for a candidate for ams in Caulobacter crescentus NA1000

Align Alpha-glucosidase; EC 3.2.1.20 (characterized, see rationale)
to candidate CCNA_02368 CCNA_02368 alpha-glucosidase

Query= uniprot:H3K096
         (538 letters)



>FitnessBrowser__Caulo:CCNA_02368
          Length = 547

 Score =  556 bits (1434), Expect = e-163
 Identities = 269/506 (53%), Positives = 345/506 (68%), Gaps = 14/506 (2%)

Query: 4   NMMWWRGGVIYQIYPRSFLDSRGDGVGDLNGITEKLDYVASLNVDGIWLSPFFTSPMLDF 63
           N  WWRG VIYQ+YPRSF DS GDGVGDL GIT  LD++ASL V+G+WLSPFFTSPM DF
Sbjct: 23  NAEWWRGAVIYQVYPRSFADSNGDGVGDLPGITAHLDHIASLGVEGVWLSPFFTSPMKDF 82

Query: 64  GYDVSDYRDVDPMFGTLEDFKALLEKAHSLGLKVMIDQVISHTSDQHPWFQESRQNRTNP 123
           GYDVS+Y DVDP+FGTL DF AL+ +AH+LGLK++ID V SHTSD+HPWF ESRQ+R+N 
Sbjct: 83  GYDVSNYCDVDPIFGTLADFDALIARAHALGLKIIIDLVFSHTSDEHPWFVESRQDRSNA 142

Query: 124 KADWFVWADPKPDGTPPNNWLSIFGGSAWTFDSRRQQYYLHNFLTSQPDVNFHHPEARQA 183
           KADWFVWAD KPDG+PP+NW S+FGG AWT+D+RR QYY+HNFL+SQP +N H+P  ++A
Sbjct: 143 KADWFVWADAKPDGSPPSNWQSVFGGPAWTWDARRGQYYMHNFLSSQPQLNLHNPAVQEA 202

Query: 184 QLDNMRFWLDLGVDGFRLDTVNFYFHDAELRDNPPVPKGEAKTLGAPEANPYTWQRHVYD 243
            L   +FW+D GVDGFR D +NF  HD  L DNPP+P G  +T       P+ +Q  +++
Sbjct: 203 LLAVTQFWIDKGVDGFRFDAINFSMHDPALTDNPPLPPGGKRT------RPFDFQDKIHN 256

Query: 244 LSRPENLDFLKDLRALMDEYPGTTTVGEIGDDNPLERMAEYTAGGDKLHMAYTFDLLNMP 303
            S  +   FL  LRAL D   G  +V E+G D+    M  +TAG D+L+ AY F  L   
Sbjct: 257 QSHADIPKFLSRLRALTDAAGGRFSVAEVGGDHAEREMKLFTAGEDRLNSAYGFLYL--- 313

Query: 304 HSASYLREVIERFQRL----AGDAWPCWATSNHDVVRSATRWGADEDPHAYPKVMLAVLF 359
           ++   + E+I +   +    AG+ WP W  SNHD  R+ +RW    D  A+ ++ L +L 
Sbjct: 314 YADKLIGEMIPQGAAMWPGEAGEGWPSWTFSNHDAPRAVSRWAEGRDRKAFAELCLLLLM 373

Query: 360 SLRGSVCLYQGEELGLPEADVPFERIQDPYGKVLWPEFKGRDGCRTPMPWTDGE-QGGFS 418
            LRG+V +YQGEELGLP+A VPFER+QDP     WP+  GRDG RTPMPW  G    GFS
Sbjct: 374 GLRGNVFVYQGEELGLPQAHVPFERLQDPEAIANWPQTLGRDGARTPMPWVSGALNAGFS 433

Query: 419 PVEPWLPMEARHLELAVSRQQDDPNATLNTVRALLAFRRSHPALFDGDLSLVDVGDDLLG 478
            VEPWLP++  HL LAV  Q+ DP +TLN  R L+  RR++PAL  G ++ +D    LL 
Sbjct: 434 GVEPWLPVDPEHLPLAVDAQEADPASTLNVARRLIGLRRAYPALRTGAITFIDTNSPLLI 493

Query: 479 FTRQKGDETLLCVFNLTGQEQQTTLP 504
           F R +G + +L  FNL  +    +LP
Sbjct: 494 FQRGEGADAVLLAFNLGFETVTWSLP 519


Lambda     K      H
   0.320    0.138    0.443 

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: 997
Number of extensions: 50
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: 538
Length of database: 547
Length adjustment: 35
Effective length of query: 503
Effective length of database: 512
Effective search space:   257536
Effective search space used:   257536
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: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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, 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

GapMind for catabolism of small carbon sources