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 sucrose hydrolase (SuxB;XCC3359) (EC 3.2.1.-) (characterized)
to candidate CCNA_01193 CCNA_01193 amylosucrase

Query= CAZy::AAM42629.1
         (637 letters)



>FitnessBrowser__Caulo:CCNA_01193
          Length = 609

 Score =  445 bits (1144), Expect = e-129
 Identities = 265/616 (43%), Positives = 339/616 (55%), Gaps = 25/616 (4%)

Query: 27  ATLARFDTHAPRLLDALSTLYGDHADYVTWLPQWLSALGVVAQARPAALRHLDDSRA--P 84
           A  ARF    P +    + LYG  A     L +  + L   A ARP  LR LD +RA  P
Sbjct: 14  AVQARFAALWPIVESRFAKLYGADARGPAVLERLKTNLLKAAHARPEPLRALDAARAADP 73

Query: 85  GWFGQQDMLGYSAYVDRFAGTLRGVAERVPYLQELGVRYLHLLPFLRARAGDNDGGFAVS 144
            W        Y+ YVDRFAG L GV  ++ YL ELGVR+LH LP L  R GD+DGGFAV+
Sbjct: 74  AWLHAPGQTAYTFYVDRFAGDLNGVRGKLDYLTELGVRWLHPLPLLEPRPGDSDGGFAVA 133

Query: 145 DYGQVEPALGSNDDLVALTARLRAANISLCADFVLNHTADDHAWAQAARAGDTRYLDYYH 204
           DY +V+P LG+ DDL AL   LR  ++ L  D V NHTA +HAWA  ARAGD  Y DYY 
Sbjct: 134 DYRKVDPRLGTIDDLEALAGDLRQRDMGLILDVVCNHTAREHAWAAKARAGDPAYRDYYI 193

Query: 205 HFADRNAPDQYDTTLVQVFPQTAPGNFTWVDETRQWMWTTFYPYQWDLNWSNPAVFGEMA 264
              D  +    D  L+ VFP TAPG+FT+      ++WTTFYP+QWDLN++NPAVF EM 
Sbjct: 194 VLPDAQSAAARDRELIDVFPDTAPGSFTYDAAMGGYVWTTFYPFQWDLNYANPAVFAEML 253

Query: 265 LAMLELANLGVEAFRLDSTAYLWKRPGTNCMNQPEAHTILVALRAVADIVAPSVVMKAEA 324
             ++ LA  G + FRLDS  +LWK+ GT C N P+ + I+ A RA   IVAP VV+ AEA
Sbjct: 254 EVLIFLAAKGAQGFRLDSAPFLWKQAGTTCRNLPQTYEIVEAWRAALSIVAPGVVLLAEA 313

Query: 325 IVPMAELPPYFGSGVQRGHECHLAYHSTLMAAGWSALALQRGDILQDVIAHSPPLPPNCA 384
           I  + ++ P+FG G + G  C+LAY++ +M A W+ALA     I +  +A +   P   A
Sbjct: 314 IESVEDVLPFFG-GEESG--CNLAYNNVVMTALWAALADGDAVIARRCLAVAARKPAQGA 370

Query: 385 WLSYVRCHDDIGWNVLQHEAAGTAAQPPFSLREVAQFYANAVPGSYARGESFQSSGDGVH 444
           WL+YVRCHDD+ WN L       A  P   LR  +  Y N     ++RG +FQ++  GV 
Sbjct: 371 WLNYVRCHDDLIWNAL------AAYAPASDLRRWSNAYGNG--EGFSRGRAFQTAEGGVP 422

Query: 445 GTNGMSAALVGVQAAHEHADAAAAARAVDRLVLLYAVSLAMPGVPLIYMGDELALPNDTA 504
            TNGM+AAL G+      ADA        RL LLY +  A+ G PLIYMGDE+ L ND A
Sbjct: 423 STNGMAAALAGLT-----ADADGDCLGARRLRLLYGIIHALDGWPLIYMGDEIGLDNDEA 477

Query: 505 YLDDAQRRHEGRWLHRPAMAWELAAQRHDASTLAGTVYTRLRALIRLRAGLPALAATQSL 564
           Y DD  R  +GRWLHRP M W LA +R +A  L   ++     L +    L  L      
Sbjct: 478 YQDDPLRAGDGRWLHRPQMDWSLAERRGEAGALQADLFATFARLGQRARRLATLGVAGPA 537

Query: 565 GSVALGDARLFALTRGDS---FLAVHNFSDVPLPVDLTQTGHALWAVLDTDGTGDAPEPH 621
             V +    + A  R +    FL V N SD P   +L       +A    D    AP P 
Sbjct: 538 RPVEVSSPAVLAFLRDEGARPFLCVANVSDAPQDFELPPA----FAQGAEDVLDGAPSPA 593

Query: 622 TELLLPAYGVRWLQRR 637
             + LP YG+ WL  R
Sbjct: 594 GAVSLPPYGITWLVAR 609


Lambda     K      H
   0.321    0.134    0.422 

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: 1202
Number of extensions: 64
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: 637
Length of database: 609
Length adjustment: 37
Effective length of query: 600
Effective length of database: 572
Effective search space:   343200
Effective search space used:   343200
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: 54 (25.4 bits)

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

Downloads

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

Related tools

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

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