GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaF in Novosphingobium barchaimii LL02

Align 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_059151871.1 V474_RS12920 enoyl-CoA hydratase

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



>NCBI__GCF_001046635.1:WP_059151871.1
          Length = 255

 Score =  150 bits (380), Expect = 2e-41
 Identities = 93/251 (37%), Positives = 137/251 (54%), Gaps = 4/251 (1%)

Query: 8   DAPEQGVRLITLQRPEALNALNTQLLDELAAELALAEQDAETRAVVLTGSR-KAFAAGAD 66
           DA E G+ +ITL RPE  NAL  ++ + L A  A  E D   R  +LTGS  KAF AG D
Sbjct: 8   DAREDGIAVITLNRPEQRNALTAEVREGLRAAWARFEADDALRIAILTGSGDKAFCAGGD 67

Query: 67  IKEMAERDLVGILEDPRVAHWQRIAAFSKPLIAAVNGFCLGGGCELAMHADILIAGEDAR 126
           +KEM E  +     D     +  I   SKP IAAVNG    GG  +A   D+ +A   A+
Sbjct: 68  LKEMVETGMAVPPRDMYALPYDTIE-LSKPTIAAVNGVAFAGGWMIAQACDLCVASTAAK 126

Query: 127 FGQPEINLGIMPGAGGTQRLLRAVGKSLAMQMVLSGQAIDARHAQRAGLVSEVTLPELTI 186
           F   E+ +G   G+     L+  +G+ + M++VL+G+ IDA  A   GLV+ +  P   +
Sbjct: 127 FAITEVKVG--RGSPWAAPLIHMIGQRIFMEIVLTGKPIDAARAYEIGLVNRLAQPGAVL 184

Query: 187 ERALAIARVIAQKAPLAVRLAKEALLKAEDTDLASGLRFERHAFTVLAGTADRAEGIRAF 246
           + A+ +AR + + APL+V+ A+E ++ + +   ++ L   R A      + D  EG RAF
Sbjct: 185 DAAIELAREVLEGAPLSVKAARETVMLSTEMGRSAALAAARSAHEHTYNSQDAQEGPRAF 244

Query: 247 QEKRRPEFTGR 257
            EKRRP ++GR
Sbjct: 245 AEKRRPVWSGR 255


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: 158
Number of extensions: 12
Number of successful extensions: 4
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: 255
Length adjustment: 24
Effective length of query: 233
Effective length of database: 231
Effective search space:    53823
Effective search space used:    53823
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 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