GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaK in Methanoculleus horonobensis T10

Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate WP_067076571.1 MCUHO_RS08130 acyl--CoA ligase

Query= BRENDA::A7KUK6
         (562 letters)



>NCBI__GCF_001602375.1:WP_067076571.1
          Length = 526

 Score =  181 bits (458), Expect = 8e-50
 Identities = 161/530 (30%), Positives = 255/530 (48%), Gaps = 60/530 (11%)

Query: 41  TQRHYTYKSLRDASLDFGKGLKALYEWRKGDVLALFTPNSIDTPVVMWGTLWAGGTIS-P 99
           T   YT   L D     G+GL  L   R GD + ++  +S +  +V +  LW  G ++ P
Sbjct: 25  TGESYTRAELLDRVCRVGRGLLDLGVGR-GDRVCIYLDSSTEY-LVSYFALWRIGAVAVP 82

Query: 100 ANPGYTVDELAFQLKNSHAKGLVTQASVLPVAREAAKKVGMPEDRIILIGDQRDPDARVK 159
            N  Y   E+ + ++++ A  ++T A                 +   L+G  RD  + ++
Sbjct: 83  TNRVYRESEVLYAVRDAGAVAVITDA-----------------EGAALVGRIRDQASTLR 125

Query: 160 HFTSVRN-ISGATRYRKQKITPAK---------DVAFLVYSSGTTGVPKGVMISHRNIVA 209
           H  +V    +GA  +      P           D+  + Y+SGTTG PKG M++H N +A
Sbjct: 126 HVVAVGGEAAGAMPWADLLRAPPDCRAVHCRFDDLCQIQYTSGTTGKPKGAMLTHGNWIA 185

Query: 210 NIRQQFIAEGEMLSWNGGPDGKGDRVLAFLPFYHIYGLTCLITQALYKGYHLIVMSKFDI 269
            +     AE ++L          D  L   P  H+ GL+  I   L  G   +VM +F++
Sbjct: 186 AMD----AERDVLRITDA-----DVYLGIYPMGHV-GLSWGIA-TLRAGGTYVVMERFEL 234

Query: 270 EKWCAHVQNYRCSFSYIVPPVVLLLGKHPVVDKYDLSSLRMMNSGAAPLTQELVEAVYSR 329
           +++    ++YR +    +PPV+  L + P   +  L++ R M SG  PLT  + +  + R
Sbjct: 235 DRYLDLARDYRATIVAGMPPVIHSLIQTPPGTETALATARAMISGGGPLTPGVWKPFHER 294

Query: 330 IKVGIKQGYGLSETSP--TTHSQRWEDWREA--MGSVGRLMPNMQAKYMTMPEDGSEP-K 384
             + I   YGLSET    T  + R E +  A    SVG  +   + K +    D ++P +
Sbjct: 295 FGIPIVNAYGLSETVVVGTGTAIRPEHYATADEFRSVGTPVGFSEVKIV----DANDPAQ 350

Query: 385 EVGEGEVGELYLKGPNVFLGYHENPEATKGCLSEDGWFQTGDVGYQDAKGNFYITDRVKE 444
           E+  G  GE+ L+GP V LGY + PE T      DGWF TGD+G+ D  G  YITDR K+
Sbjct: 351 ELRPGVDGEIALRGPGVALGYWQMPEETAAVFLPDGWFLTGDIGHLDEDGMLYITDRKKD 410

Query: 445 LIKYKGFQVPPAELEGYLVDNDAIDDVAVIGIESETHGSEVPMACVVRSAKSKSSGTSEK 504
           +I   G++V P E+E  LV +  + D AV G   E H  EVP+A VV       +G S  
Sbjct: 411 MIVMSGWKVYPTEVEDVLVQHPGVRDAAVFGCTDE-HRGEVPVAVVV----PVGNGISPD 465

Query: 505 DEAARIIKWLDSKVASHKRLRGGVHFVDEIPKNPSGKILRRILKQKFKGA 554
           +    I+ +   ++A +K  R  V   +EIP+    K+LR+ L++++ GA
Sbjct: 466 E----IVAFARERLAGYKVPR-RVIIAEEIPRVNGWKLLRKRLREEYCGA 510


Lambda     K      H
   0.317    0.136    0.410 

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: 732
Number of extensions: 38
Number of successful extensions: 5
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: 562
Length of database: 526
Length adjustment: 35
Effective length of query: 527
Effective length of database: 491
Effective search space:   258757
Effective search space used:   258757
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 (21.7 bits)
S2: 52 (24.6 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