GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Pseudomonas putida KT2440

Align isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate PP_4063 PP_4063 putative Long-chain-fatty-acid-CoA ligase

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



>FitnessBrowser__Putida:PP_4063
          Length = 560

 Score =  164 bits (415), Expect = 8e-45
 Identities = 156/563 (27%), Positives = 243/563 (43%), Gaps = 64/563 (11%)

Query: 24  ATVYGDCTSVV----YDAVSYTWSQTHRRCLCLASSIASLGIENGHVVSVLAPNVPQMYE 79
           ATV   C S      +  + Y+W Q   +    A ++ +LG+  G  V + +PN  Q   
Sbjct: 26  ATVARCCDSEALVSRHQGLRYSWRQLAEQVEIYARALIALGVNTGDRVGIWSPNCAQWCI 85

Query: 80  LHFAVPMAGAILNAVNLRLDARTISILLHHSESKLIFVDHLSRDLILEAIALFPKQAPVP 139
           L  A    GAIL  +N       +  +L  S  + +        +  EA         V 
Sbjct: 86  LQLASAKVGAILVNINPAYRVGELEYVLRQSGCRWL--------VCAEAFKTSDYHTMVQ 137

Query: 140 RLVFMADESESGNSSELGKEFFCSYKDLIDRGDPDFKWVMPKSEW--------------- 184
            LV    E  S    EL  E     + +I          +P   +               
Sbjct: 138 ELV---PELASAAPGELASECLPELRGVISLAANPPAGFLPWHAFAERAGQTSVEACTAR 194

Query: 185 -------DPMILNYTSGTTSSPKGVVHCHRGIF---IMTVDSLIDWGVPKQPVYLWTLPM 234
                   P+ + YTSGTT +PKG    H  I     M  +SL   G+  +   +  +P+
Sbjct: 195 QQSLQFDQPVNIQYTSGTTGAPKGATLSHYNILNNGFMVGESL---GLTARDRMVIPVPL 251

Query: 235 FHANGWSYP-WGMAAVGGTNICLRK-FDSEIIYDMIKRHGVTHMCGAPVVLNMLSNAPGS 292
           +H  G      G    G T I     FD+E+    +     T + G P +   + + P  
Sbjct: 252 YHCFGMVMANLGCITHGSTMIYPNDAFDAELTLRAVAEERATILYGVPTMFIAMLDHPSR 311

Query: 293 E--PLKTTVQIMTAGAPPPSAVLFRT-ESLGFA-VSHGYGLTETAGLVVSCAWKKEWNHL 348
               L T    + AGA  P  V+ R  + +  A V   YG+TET+ + +      +   L
Sbjct: 312 AHMDLSTLRSGIMAGATCPIEVMRRVIDQMHMAEVQIAYGMTETSPVSLQTGPDDDLE-L 370

Query: 349 PATERARLKSRQGVGTVMQTKIDVVDPVTGAAVKRDGSTLGEVVLRGGSVMLGYLKDPEG 408
             T   R        T  Q +  +VD   G  V R    +GE+  RG SVMLGY  +P+ 
Sbjct: 371 RVTTVGR--------TQPQLENKLVD-ADGCIVPR--GEIGELCTRGYSVMLGYWDNPQA 419

Query: 409 TAKSMTADGWFYTGDVGVMHPDGYLEIKDRSKDVIISGGENLSSVEVESILYSHPDILEA 468
           TA ++   GW ++GD+ VM   GY+ I  R+KD+II GGEN+   E+E   Y+HP + +A
Sbjct: 420 TADAIDPAGWMHSGDLAVMDEQGYVRIVGRNKDMIIRGGENIYPRELEEFFYTHPAVADA 479

Query: 469 AVVARPDEFWGETPCAFVSLKKGLTKKPTEKEIVEYCRSKLPRYMVPKTVVFKEELPKTS 528
            V+  P   +GE   A++ L  G     T +E+  +C++++  + VP+ + F +E P T 
Sbjct: 480 QVIGIPCSRYGEEIVAWIKLHPG--HSATVEELQGWCKARIAHFKVPRYIRFVDEYPMTV 537

Query: 529 TGKVQKFILRDMA-RGMGSATAG 550
           TGKVQKF +R+++   + +A+AG
Sbjct: 538 TGKVQKFRMREISVAEIAAASAG 560


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: 752
Number of extensions: 44
Number of successful extensions: 4
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: 556
Length of database: 560
Length adjustment: 36
Effective length of query: 520
Effective length of database: 524
Effective search space:   272480
Effective search space used:   272480
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 (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