GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acs in Pseudomonas simiae WCS417

Align isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate GFF4309 PS417_22070 long-chain fatty acid--CoA ligase

Query= metacyc::MONOMER-20125
         (556 letters)



>lcl|FitnessBrowser__WCS417:GFF4309 PS417_22070 long-chain fatty
           acid--CoA ligase
          Length = 562

 Score =  135 bits (340), Expect = 4e-36
 Identities = 114/377 (30%), Positives = 174/377 (46%), Gaps = 42/377 (11%)

Query: 185 DPMILNYTSGTTSSPKGVVHCH----------RGIFIMTVDS---LIDWGVPKQPVYLWT 231
           D  +L YT GTT   KG +  H          R     T D    LI  G   Q V +  
Sbjct: 208 DIAVLQYTGGTTGLAKGAMLTHGNLVANMQQVRACMSQTGDDGHPLIKEG---QEVMIAP 264

Query: 232 LPMFHANGWSYPWGMAAVGGTNICLRKFDSEI--IYDMIKRHGVTHMCGAPVVLNMLSNA 289
           LP++H   ++       V G +  L     +I      +K+   T + G   +   L + 
Sbjct: 265 LPLYHIYAFTANCMCMMVSGNHNVLITNPRDIGGFIKELKKWRFTGLLGLNTLFVALMDH 324

Query: 290 PGSEPLKTTVQIMT--AGAPPPSAVLFRTESL-GFAVSHGYGLTETAGLVVSCAWKKEWN 346
           P  + L  +   +T   G     A   R + + G A+  GYGLTET+ +           
Sbjct: 325 PDFKSLDFSHLKLTNSGGTALIKATAERWQQITGCAIGEGYGLTETSPVA---------- 374

Query: 347 HLPATERARLKSRQG-VGT-VMQTKIDVVDPVTGAAVKRDGSTLGEVVLRGGSVMLGYLK 404
              +T     KSR G VG  V  T + V+D      V+      GE+ ++G  VM GY +
Sbjct: 375 ---STNPYGNKSRLGTVGIPVPATAMKVIDD---HGVELPLGERGELCIKGPQVMKGYWQ 428

Query: 405 DPEGTAKSMTADGWFYTGDVGVMHPDGYLEIKDRSKDVIISGGENLSSVEVESILYSHPD 464
            PE TA+++ A+GW  TGD+ V+  +G++ I DR KD+II  G N+   E+E ++ +HP 
Sbjct: 429 QPEATAEALDAEGWLKTGDIAVIDEEGFVSIVDRKKDLIIVSGFNVYPNEIEDVVMAHPA 488

Query: 465 ILEAAVVARPDEFWGETPCAFVSLKKGLTKKPTEKEIVEYCRSKLPRYMVPKTVVFKEEL 524
           +   AV+  PDE  GE    FV  +    +  + +E+  YC++    Y VPK +V ++ L
Sbjct: 489 VANCAVIGVPDERTGEAVKLFVVAR---AEGVSLEELKAYCKTNFTGYKVPKHIVLRDSL 545

Query: 525 PKTSTGKVQKFILRDMA 541
           P T  GK+ +  LRD+A
Sbjct: 546 PMTPVGKILRRELRDIA 562


Lambda     K      H
   0.319    0.135    0.412 

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: 756
Number of extensions: 44
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 556
Length of database: 562
Length adjustment: 36
Effective length of query: 520
Effective length of database: 526
Effective search space:   273520
Effective search space used:   273520
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 (21.7 bits)
S2: 53 (25.0 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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