GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Paludibacter propionicigenes WB4

Align isovalerate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate WP_013445999.1 PALPR_RS12485 AMP-binding protein

Query= metacyc::MONOMER-20124
         (573 letters)



>NCBI__GCF_000183135.1:WP_013445999.1
          Length = 549

 Score =  177 bits (448), Expect = 1e-48
 Identities = 147/548 (26%), Positives = 242/548 (44%), Gaps = 43/548 (7%)

Query: 47  FLERSSKAYRDNTSLVYG--SVRYTWAQTHHRCLKLASALTTHLGISPGDVVATFSYNLP 104
           +LE  +    D+  +VY   ++R++W+  + R   +A  L   +G++ G  V  ++ N+P
Sbjct: 11  WLEHWAAETPDHEYIVYSDRNLRFSWSAFNERVDNMAKGLLA-VGVTKGCHVGIWAQNVP 69

Query: 105 EIYELHFAVPMAGGILCTLNARNDSAMVSTLLAHSEAKLI----------FVE------P 148
           +     +A    G +  T+N       ++ +L +S+   +          +VE      P
Sbjct: 70  DWLTFLYACAKLGAVAVTVNTNYKDHELAFVLENSDMHTLCITDGISGSDYVEMVYSLIP 129

Query: 149 QLLETARAALDLLAQKDIKPPTLVLLTDSESFTSSSYDHYNHLLANGSDD----FEIRRP 204
           +L    R  L      ++K    +     +      Y+    LL   +       +I++ 
Sbjct: 130 ELKTNQRGHLKSERFPELKNVIYI----GQEKHRGMYNTAEVLLLGDNQPNDAFLKIKKS 185

Query: 205 KNEWDPISINYTSGTTARPKAVVYSHRGAYLNSIATVLLHGMGTTSVYLWSVPMFHCNGW 264
            +  + +++ YTSGTT  PK V+ SH     N   T               VP+FHC G 
Sbjct: 186 VSCHEVVNMQYTSGTTGFPKGVMLSHHNIANNGYLTGEHMKFTQADKLCVCVPLFHCFGV 245

Query: 265 CFP-WGAAAQGATNICIRKVSPKAIFDNIHLHKVTHFGAAPTVLNMIVNSPEGNLHTPLP 323
                     G T + + K  P     +IH  + T     PT+    +N P   L     
Sbjct: 246 VLATMNCLTHGCTQVMVEKFDPLITLASIHKERCTAVYGVPTMFIAELNHPMFELFDMSS 305

Query: 324 HKVEVMTGGSPPPPKVIARMEEMGFQVNHIYGLTETCGPAANCVCKPEWDALQPEERYAL 383
            +  +M G   P   +    E+M   +  +YGLTET          P     + E+ + +
Sbjct: 306 LRTGIMAGALCPIELMRQVSEKMFMTITSVYGLTET---------SPGMTQTRLEDSFEV 356

Query: 384 KARQGLNHLAMEEMDVRDPVTMESVRADGATIGEVMFRGNTVMSGYFKDLKATEEAFE-G 442
           +     +     E+ V +P T E +  DG   GE+  RG  VM GY+K+ +AT E  +  
Sbjct: 357 RCTTVGSDYEFTEVAVINPETGE-ICPDGVQ-GEMCCRGYNVMKGYYKNPQATSEVIDKN 414

Query: 443 GWFRSGDLGVKHEDGYIQLKDRKKDVVISGGENISTVEVETVLYSHEAVLEAAVVARPDK 502
           G+ RSGDLGVK  DG  ++  R KD++I GGENIS  E+E  LY    V +A +VA    
Sbjct: 415 GYLRSGDLGVKDLDGNYRITGRIKDMIIRGGENISPREIEEFLYHMPGVKDAQIVALASP 474

Query: 503 LWGETPCAFVTLKEGFDNDVSADQIIKFCRDRLPHYMAPKTVVF-EELPKTSTGKIQKYI 561
            +GE   AF+    G+   ++ + +  FC+D++  Y  P+ V F  E P T +GKIQK+ 
Sbjct: 475 RYGEDVAAFIIQHAGY--QLTLEDVRDFCKDKIARYKIPRYVFFVSEYPLTGSGKIQKFK 532

Query: 562 LKEKAMAM 569
           L+E A+ +
Sbjct: 533 LREMAIEL 540


Lambda     K      H
   0.318    0.133    0.408 

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: 715
Number of extensions: 37
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 573
Length of database: 549
Length adjustment: 36
Effective length of query: 537
Effective length of database: 513
Effective search space:   275481
Effective search space used:   275481
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: 53 (25.0 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