GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaE in Pedobacter sp. GW460-11-11-14-LB5

Align 1,2-phenylacetyl-CoA epoxidase, subunit E; 1,2-phenylacetyl-CoA epoxidase, reductase subunit; 1,2-phenylacetyl-CoA monooxygenase, subunit E; EC 1.-.-.- (characterized)
to candidate CA265_RS25075 CA265_RS25075 phenylacetic acid degradation protein

Query= SwissProt::P76081
         (356 letters)



>FitnessBrowser__Pedo557:CA265_RS25075
          Length = 348

 Score =  154 bits (390), Expect = 3e-42
 Identities = 112/355 (31%), Positives = 164/355 (46%), Gaps = 25/355 (7%)

Query: 7   LTVAKVESETRDAVTITFAVPQPLQEAY-RFRPGQHLTLKASFDGEELRRCYSICRSYLP 65
           L + K+ ++  D +T  F   + + E Y ++  GQ ++L      +E+RR YS   S   
Sbjct: 4   LRINKIINQPGDNITFQF---EEVDEPYPKYLAGQFISLIFQGKHKEIRRSYSFNSSPDV 60

Query: 66  GE-ISVAVKAIEGGRFSRYAREHIRQGMTLEVMVPQGHFGYQPQAERQGRYLAIAAGSGI 124
            E +S+ VK +E G  SR+          L    PQG F Y P    +      AAG GI
Sbjct: 61  DEPLSITVKRVENGEISRFLHHKTSVNDILLAQEPQGMFSYLPDENLERDLFLFAAGVGI 120

Query: 125 TPMLAIIATTLQTEPESQFTLIYGNRTSQSMMFRQALADLKDKYPQRLQLLCIFSQETLD 184
           TP+ +I+ T L  E +S  TL+Y NR+ +  +F   L++ + KYP+RL+++ +FS     
Sbjct: 121 TPLFSILKTALVREKKSLVTLVYSNRSMEDALFYDELSEWQKKYPERLKIVWVFSN---S 177

Query: 185 SDLLHGRIDGEKLQSLGASLINFRLYDEAFI-CGPAAMMDDAETALKALGMPDKTIHLER 243
            +L+  R++   ++ L    ++F   D  F  CGP   MD     L  +G   K I  E 
Sbjct: 178 KNLMTARLNKFYIEKLLKEHLHFDRNDALFYSCGPIIYMDLCRITLLGVGFDIKQIKRET 237

Query: 244 FNTPGTRVKRSVNVQSDGQKVTVRQDGRDREIVLNADDE----------SILDAALRQGA 293
           F  P   V      + DG    V  D     +VLN   E           ILD AL    
Sbjct: 238 FVLPEDEVD-----EDDGSAEKV-VDKNTYSVVLNFKGEIYHLDVPWPKRILDVALENKI 291

Query: 294 DLPYACKGGVCATCKCKVLRGKVAMETNYSLEPDELAAGYVLSCQALPLTSDVVV 348
            LPY+C+GGVC+TC     +G V M+ N  L  DEL  G VL C   P  +   +
Sbjct: 292 KLPYSCRGGVCSTCVANCTKGGVRMDYNEVLTDDELERGRVLVCTGHPTENGTTI 346


Lambda     K      H
   0.320    0.135    0.390 

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: 289
Number of extensions: 11
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: 356
Length of database: 348
Length adjustment: 29
Effective length of query: 327
Effective length of database: 319
Effective search space:   104313
Effective search space used:   104313
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: 49 (23.5 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