GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaF in Pseudomonas fluorescens GW456-L13

Align 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate PfGW456L13_2434 Phenylacetate degradation enoyl-CoA hydratase PaaA (EC 4.2.1.17)

Query= metacyc::MONOMER-15953
         (257 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2434
          Length = 257

 Score =  404 bits (1039), Expect = e-118
 Identities = 212/257 (82%), Positives = 228/257 (88%)

Query: 1   MPHTLSVDAPEQGVRLITLQRPEALNALNTQLLDELAAELALAEQDAETRAVVLTGSRKA 60
           MP TL+V+  E GVRLITLQRP+ALNAL T+LL ELAAEL +A+ D +TRAVVLTGSRKA
Sbjct: 1   MPLTLAVELIEPGVRLITLQRPQALNALTTELLGELAAELNIAQADPDTRAVVLTGSRKA 60

Query: 61  FAAGADIKEMAERDLVGILEDPRVAHWQRIAAFSKPLIAAVNGFCLGGGCELAMHADILI 120
           FAAGADIKEMAERDLVGIL+DPR A WQ I  FSKPLIAAVNGF LGGGCELAMHADI+I
Sbjct: 61  FAAGADIKEMAERDLVGILDDPRQASWQAITRFSKPLIAAVNGFALGGGCELAMHADIII 120

Query: 121 AGEDARFGQPEINLGIMPGAGGTQRLLRAVGKSLAMQMVLSGQAIDARHAQRAGLVSEVT 180
           AGEDARFGQPEINLGIMPGAGGTQRLLRAVGKS+AMQMVL+G++IDAR AQR GLVSEVT
Sbjct: 121 AGEDARFGQPEINLGIMPGAGGTQRLLRAVGKSMAMQMVLTGESIDARQAQRVGLVSEVT 180

Query: 181 LPELTIERALAIARVIAQKAPLAVRLAKEALLKAEDTDLASGLRFERHAFTVLAGTADRA 240
            PE T+ERAL IA  IA KAPLAVRLAKEALLKA DTDLA+GLRFERHAFTVLAGT DR 
Sbjct: 181 QPEFTVERALHIAHSIAAKAPLAVRLAKEALLKAMDTDLATGLRFERHAFTVLAGTRDRD 240

Query: 241 EGIRAFQEKRRPEFTGR 257
           EGI AFQEKR P FTG+
Sbjct: 241 EGIAAFQEKRSPTFTGQ 257


Lambda     K      H
   0.320    0.134    0.374 

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: 315
Number of extensions: 11
Number of successful extensions: 1
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: 257
Length of database: 257
Length adjustment: 24
Effective length of query: 233
Effective length of database: 233
Effective search space:    54289
Effective search space used:    54289
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: 47 (22.7 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