GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimB in Caulobacter crescentus NA1000

Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate CCNA_03575 CCNA_03575 3-ketoacyl-CoA thiolase

Query= metacyc::MONOMER-20679
         (395 letters)



>FitnessBrowser__Caulo:CCNA_03575
          Length = 395

 Score =  487 bits (1253), Expect = e-142
 Identities = 252/394 (63%), Positives = 296/394 (75%), Gaps = 1/394 (0%)

Query: 1   MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQ 60
           M EAVIVS ART + K+ RG  N T GA + GHAI+HAV RAG++  EVEDVV+G    +
Sbjct: 1   MREAVIVSYARTGLAKSVRGGFNNTHGAAMAGHAIQHAVSRAGLEGAEVEDVVLGCGGPE 60

Query: 61  GATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESI 120
           GATG N+AR A + AGLPVTT+G TI+R C+SGLQAIA AA  V  DG  +A+GGG ESI
Sbjct: 61  GATGMNVARNAAMWAGLPVTTSGQTINRFCSSGLQAIATAANYVRNDGANVAIGGGVESI 120

Query: 121 SLVQ-NDKMNTFHAVDPALEAIKGDVYMAMLDTAETVAKRYGISRERQDEYSLESQRRTA 179
           SLV     MN FH  +  L      ++MAM+DTA+ VAKRY +SRE QDEY+L SQ+R A
Sbjct: 121 SLVNAGGHMNRFHITEEKLMQTHPALWMAMIDTADIVAKRYNVSREYQDEYALRSQQRIA 180

Query: 180 AAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGLKAVRGE 239
           AAQ  G F DEI P++TKM VV+K T   SF D  + +DE  R +TT EGLA LK V GE
Sbjct: 181 AAQAAGLFKDEIVPMATKMKVVNKETKEESFVDYVVDKDECNRADTTLEGLASLKPVMGE 240

Query: 240 GFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMGIGPVFAVP 299
           G  ITAGNASQLSDGA+A V+M  K A  +GL PLG FRG    GCEPDEMGIGPVFAVP
Sbjct: 241 GKFITAGNASQLSDGAAAVVVMEAKEAEKRGLTPLGAFRGFAVAGCEPDEMGIGPVFAVP 300

Query: 300 RLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGHPYGMSGARL 359
           RLL+RHGL VDDI +WELNEAFA Q LY RD+LGIDPEK NVNGG+I++GHP+GM+GAR 
Sbjct: 301 RLLERHGLKVDDIDIWELNEAFASQCLYSRDRLGIDPEKYNVNGGSIAIGHPFGMTGARC 360

Query: 360 AGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEI 393
           AGH L+EG+RRKAK  VVTMC+GGGMG+AGLFEI
Sbjct: 361 AGHLLLEGKRRKAKLGVVTMCIGGGMGAAGLFEI 394


Lambda     K      H
   0.316    0.134    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: 526
Number of extensions: 18
Number of successful extensions: 2
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: 395
Length of database: 395
Length adjustment: 31
Effective length of query: 364
Effective length of database: 364
Effective search space:   132496
Effective search space used:   132496
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 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