GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaA in Phaeobacter inhibens BS107

Align ring 1,2-phenylacetyl-CoA epoxidase PaaA subunit (EC 1.14.13.149) (characterized)
to candidate GFF397 PGA1_c04080 phenylacetic acid degradation protein PaaA

Query= metacyc::MONOMER-15947
         (330 letters)



>FitnessBrowser__Phaeo:GFF397
          Length = 325

 Score =  467 bits (1201), Expect = e-136
 Identities = 223/330 (67%), Positives = 267/330 (80%), Gaps = 6/330 (1%)

Query: 1   MYAQLVETGVKRVKALEEMAPEERAFQERIDAEIKIEAKNWMPDAYRQTLIRQISQHAHS 60
           MYAQ+V++     +A ++   +  AFQ RIDA  KIE K+WMP+ YR+TLIRQI QHAHS
Sbjct: 1   MYAQMVKS-----EATQDDPEQLAAFQARIDAGEKIEPKDWMPEGYRKTLIRQIGQHAHS 55

Query: 61  EIVGMLPEGNWVTRAPTLKRKLQLMAKIQDEAGHGLYLYSAMETLGADRDEEIAKLHSGK 120
           EIVG LPEGNW+TRAPTL+RK  L+AK+QDEAGHGLYLY A ETLG  RDE    L  G+
Sbjct: 56  EIVGQLPEGNWITRAPTLERKAILLAKVQDEAGHGLYLYCAAETLGVSRDEMTEMLLDGR 115

Query: 121 AKYSSIFNYPTLNWADMGAVGWLVDGAAIVNQVVLQRTSYGPYSRAMIRICKEESFHQRQ 180
            KYSSIFNYPTLNWAD+GAVGWLVDGAAI+NQV LQRTS+GPYSRAMIR+CKEESFHQRQ
Sbjct: 116 MKYSSIFNYPTLNWADIGAVGWLVDGAAIMNQVPLQRTSFGPYSRAMIRVCKEESFHQRQ 175

Query: 181 GYEILLTMMRHGTQAQKDMVQDAINRLWWPALMMFGPSDEHSPNSAQSMAWKIKRQSNDE 240
           GY+  +  M  GT AQK M QDA+NRLW+P+LMMFGPSD+ S +SAQSMAWKIK  +NDE
Sbjct: 176 GYD-AIRKMAEGTPAQKKMAQDALNRLWYPSLMMFGPSDKDSVHSAQSMAWKIKMNTNDE 234

Query: 241 LRQRFIDQTVPQLELLGCTAPDPELKWNEERGHYDFGAIDWSEFYEVLKGNGPCNAERIA 300
           LRQ+F+DQTVPQ E LG T PDP+LKWNEERGHYD+   DW+EF++V+KGNGPCN +R+A
Sbjct: 235 LRQKFVDQTVPQAEYLGLTVPDPDLKWNEERGHYDYTDPDWNEFFDVIKGNGPCNVDRLA 294

Query: 301 TRRNAIDNGAWVREAAVAHARKQQHKRDAA 330
            R  A D+G WVR+  +AHA+K+  ++ AA
Sbjct: 295 ARNKAWDDGEWVRDGLLAHAKKKAAQKHAA 324


Lambda     K      H
   0.318    0.131    0.402 

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: 431
Number of extensions: 13
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: 330
Length of database: 325
Length adjustment: 28
Effective length of query: 302
Effective length of database: 297
Effective search space:    89694
Effective search space used:    89694
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 (21.7 bits)
S2: 48 (23.1 bits)

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

Links

Downloads

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:

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