GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Marinicella litoralis KMM 3900

Align Probable enoyl-CoA hydratase; EC 4.2.1.17 (uncharacterized)
to candidate WP_099020024.1 CCS90_RS13100 hypothetical protein

Query= curated2:Q52995
         (257 letters)



>NCBI__GCF_002591915.1:WP_099020024.1
          Length = 258

 Score =  208 bits (530), Expect = 8e-59
 Identities = 116/253 (45%), Positives = 161/253 (63%), Gaps = 3/253 (1%)

Query: 6   LLVETQGRVGLITLNRPQALNALNAVLMRELDAALKAFDADRAVGAIVLAGS-EKAFAAG 64
           +L + +  +  IT+NRP  LNALN   ++ELD  ++    D  V  IV+ GS +KAF AG
Sbjct: 4   VLSQLENNILTITINRPDKLNALNQATLKELDTIIQGAADDDNVACIVITGSGDKAFVAG 63

Query: 65  ADIKEMQGLDFVDGYLADFLGG--WEHVANARKPMIAAVSGFALGGGCELAMMCDFIIAS 122
           ADI E+   D + G      G   + H+ N  KP+IAAV+GFALGGGCELAM C   IAS
Sbjct: 64  ADISELATTDAMTGMKFARFGQSVFNHIENCGKPVIAAVNGFALGGGCELAMACHLRIAS 123

Query: 123 ETAKFGQPEITLGVIPGMGGSQRLTRAVGKAKAMDLILTGRMMDAAEAERSGLVSRVVAP 182
           + AKFGQPEI LGVIPG GG+QRLTR VGK+K+M++ L G M+ A +AE  GL++ VV  
Sbjct: 124 DNAKFGQPEIKLGVIPGFGGTQRLTRLVGKSKSMEMNLLGDMVSADKAEHIGLINWVVPQ 183

Query: 183 DRLLEEALGAAEKIASFSLPAAMMAKEAVNRSLELTLAEGLRFERRLFQSLFATEDQKEG 242
             L+      A+++A+ +  A  M  +A+N+ LE  L + L +E + F    A+ D+ EG
Sbjct: 184 GELMASVTQVAQQLAASAPIALSMTIDAINKGLECALPDALDYEVKAFGICCASADKNEG 243

Query: 243 MAAFVAKRKAEFK 255
            +AF+ KRKA+F+
Sbjct: 244 TSAFLEKRKAKFQ 256


Lambda     K      H
   0.321    0.134    0.371 

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: 175
Number of extensions: 9
Number of successful extensions: 3
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: 258
Length adjustment: 24
Effective length of query: 233
Effective length of database: 234
Effective search space:    54522
Effective search space used:    54522
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 (21.9 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