GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimD in Xanthobacter autotrophicus Py2

Align pimeloyl-CoA dehydrogenase large subunit (EC 1.3.1.62) (characterized)
to candidate WP_012113725.1 XAUT_RS08535 acyl-CoA dehydrogenase family protein

Query= metacyc::MONOMER-20676
         (396 letters)



>NCBI__GCF_000017645.1:WP_012113725.1
          Length = 396

 Score =  355 bits (910), Expect = e-102
 Identities = 185/399 (46%), Positives = 256/399 (64%), Gaps = 6/399 (1%)

Query: 1   MDLNFSKEEIAFRDEVRQFFKDNVPAKTRQKLIEGRHNTKEEMVEWYRILNKKGWAVTHW 60
           MD  FS  E AFR EVR F + N+PA    ++  G H ++ +M  W  IL+ KGWA  HW
Sbjct: 1   MDTFFSDAEQAFRAEVRAFIRANLPADLAARVRAGIHLSRADMARWNAILDAKGWAAHHW 60

Query: 61  PKEYGGTGWSSVQHYIFNEELQAAPAPQPLAFGVSMVGPVIYTFGSEEQKKRFLPRIANV 120
           P+ YGG GW+ +Q ++F  E   A AP    FGV +VGP +YTFGS+ QK+ +LP I + 
Sbjct: 61  PQTYGGPGWTPIQRFLFEAECADADAPPLSVFGVYLVGPTLYTFGSQAQKEAYLPGIRSG 120

Query: 121 DDWWCQGFSEPGSGSDLASLKTKAEKKGDKWIINGQKTWTTLAQHADWIFCLCRTDPAAK 180
             +WCQG+SEP +GSDLASLKT A K    ++I+G K WTT    AD++ CL RT+P AK
Sbjct: 121 ATFWCQGYSEPNAGSDLASLKTTARKVEGGYVIDGAKAWTTEGHFADYMICLARTNPQAK 180

Query: 181 KQEGISFILVDMKTKGITVRPIQTIDGGHEVNEVFFDDVEVPLENLVGQENKGWDYAKFL 240
            Q G+S  +VDM  KG++++P+ TIDG H VN  F D V VP + L+G+ +KGW YAKFL
Sbjct: 181 PQAGLSLFIVDMTAKGVSLQPVITIDGAHSVNTTFLDAVFVPDDALIGEIDKGWTYAKFL 240

Query: 241 LGNERTGIARVGMSKERIRRIKQLAAQVES-GGKPVIEDPKFRDKLAAVEIELKALELTQ 299
           L +ERT  A+V  S+    R+K+LA Q+    G  V++DP F+ + AA+++EL ALE+T 
Sbjct: 241 LSHERTNNAQVHRSRREFTRLKELARQMSGPAGGSVLDDPVFQRRFAALDVELSALEVTV 300

Query: 300 LRVVADEGKHGKGKPNPASSVLKIKGSEIQQATTELLMEVIGPFAAPYDVHG--DDDSNE 357
           LRV+AD+   G+ +P P +S+LK+ GSE+QQ  +EL MEV+G        HG  D ++  
Sbjct: 301 LRVLADQ-TDGR-EPGPEASILKVIGSELQQRISELAMEVLGEEGIRQS-HGEVDGEAGA 357

Query: 358 TMDWTAQIAPGYFNNRKVSIYGGSNEIQRNIICKAVLGL 396
                A  A  +   R V+IY G+NEIQ+ II + VLG+
Sbjct: 358 AATQAAGWAERHLFRRVVTIYAGANEIQKTIIARTVLGM 396


Lambda     K      H
   0.317    0.135    0.411 

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: 397
Number of extensions: 17
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: 396
Length of database: 396
Length adjustment: 31
Effective length of query: 365
Effective length of database: 365
Effective search space:   133225
Effective search space used:   133225
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. 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