GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaA in Kocuria flava HO-9041

Align ring 1,2-phenylacetyl-CoA epoxidase PaaA subunit (EC 1.14.13.149) (characterized)
to candidate WP_083529125.1 AS188_RS01190 1,2-phenylacetyl-CoA epoxidase subunit A

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



>NCBI__GCF_001482365.1:WP_083529125.1
          Length = 338

 Score =  441 bits (1134), Expect = e-128
 Identities = 217/321 (67%), Positives = 250/321 (77%), Gaps = 7/321 (2%)

Query: 8   TGVKRVKALE--EMAPEERAFQERIDAEI----KIEAKNWMPDAYRQTLIRQISQHAHSE 61
           TG+  V A +  E A  ERA QE  D  I    +IE ++WMP AYR+TL+RQ+SQHAHSE
Sbjct: 6   TGLHAVPAADAAEQAEAERAGQEHFDRIIAEDSRIEPRDWMPAAYRKTLVRQVSQHAHSE 65

Query: 62  IVGMLPEGNWVTRAPTLKRKLQLMAKIQDEAGHGLYLYSAMETLGADRDEEIAKLHSGKA 121
           I+GM PEGNW++RAP+LKRK  LMAK+QDEAGHGLYLYSA ETLG  R E   +L  G+A
Sbjct: 66  IIGMQPEGNWISRAPSLKRKAILMAKVQDEAGHGLYLYSAAETLGTPRHELNQQLLEGRA 125

Query: 122 KYSSIFNYPTLNWADMGAVGWLVDGAAIVNQVVLQRTSYGPYSRAMIRICKEESFHQRQG 181
           KYSSIFNYP   WADMGA+GWLVDGAAI NQV L R SYGPY RAM+RICKEESFHQRQG
Sbjct: 126 KYSSIFNYPARTWADMGAIGWLVDGAAIANQVPLCRASYGPYGRAMVRICKEESFHQRQG 185

Query: 182 YEILLTMMRHGTQAQKDMVQDAINRLWWPALMMFGPSDEHSPNSAQSMAWKIKRQSNDEL 241
           +EIL   + HGT AQK M QDA+NR + PAL MFGP DE SPNS QSMAW IKR SNDEL
Sbjct: 186 WEILYE-LSHGTPAQKKMAQDAVNRFYGPALQMFGPPDEDSPNSKQSMAWNIKRFSNDEL 244

Query: 242 RQRFIDQTVPQLELLGCTAPDPELKWNEERGHYDFGAIDWSEFYEVLKGNGPCNAERIAT 301
           RQRF+D  VPQ E LG T PDP+LKWNEERGHYD+G +DW+EF  V+ G GPC+++R+  
Sbjct: 245 RQRFVDMIVPQAEALGLTLPDPDLKWNEERGHYDYGPLDWNEFKAVIAGKGPCSSQRMQR 304

Query: 302 RRNAIDNGAWVREAAVAHARK 322
           RR A D+GAWVREAA A+ARK
Sbjct: 305 RRQAHDDGAWVREAAAAYARK 325


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: 451
Number of extensions: 19
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: 338
Length adjustment: 28
Effective length of query: 302
Effective length of database: 310
Effective search space:    93620
Effective search space used:    93620
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: 49 (23.5 bits)

This GapMind analysis is from Sep 24 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