Alignments for a candidate for prpE in Pseudomonas stutzeri RCH2

GapMind for Amino acid biosynthesis

Alignments for a candidate for prpE in Pseudomonas stutzeri RCH2

Align Acetate--CoA ligase CCL3; HlCCL3; 2-methylbutanoate--CoA ligase CCL4; 2-methylpropanoate--CoA ligase CCL4; Butanoate--CoA ligase CCL3; Hexanoate--CoA ligase CCL3; Isovalerate--CoA ligase CCL3; Pentanoate--CoA ligase CCL3; Propionate--CoA ligase CCL3; EC 6.2.1.1; EC 6.2.1.-; EC 6.2.1.17 (characterized)
to candidate GFF2429 Psest_2477 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II

Query= SwissProt::M4IS88
         (568 letters)



>FitnessBrowser__psRCH2:GFF2429
          Length = 542

 Score =  156 bits (394), Expect = 2e-42
 Identities = 160/552 (28%), Positives = 241/552 (43%), Gaps = 54/552 (9%)

Query: 27  LERAATVHPTRTSVIHGSRHYTWLQTYHRCRQFASALNNHSIGLGST----VAVIAPNVP 82
           L+R A   P + ++ +  R +++ Q   R    A+ + NH + LG +    VA    N  
Sbjct: 20  LQRIAMRSPEQIALQYRERRWSF-QALDRA---ANRVANHLLALGLSKADRVAAYGKNSD 75

Query: 83  ALYEAHFAVPMAGAVVNCVNIRLNASTIAFLLGHSSAAAVMVDQEFFSLAEE--ALKILA 140
           A      A   AG +   VN  L    +A++L  S A A+ VD     L +   A + LA
Sbjct: 76  AYLILWLACTRAGLIHVPVNYSLTEHELAYVLDQSGARALFVDDSLKGLVDRIPAQRQLA 135

Query: 141 QESKSHYKPPLLVVIGDESCDPKTLEYALKTGAIEYEKFLEGGDPEFDWKPPED--EWQS 198
                H          +E+   ++    + TG+              D  P  D  E   
Sbjct: 136 IRGSLH---------SNETTSDRSDILRIATGSA------------CDLPPEVDIAETDV 174

Query: 199 ISLGYTSGTTASPKGVVLSHRGAYLMSLSASVVWGINEGAIYLWTLPMFHCNGWCYTWGM 258
           + + YTSGTT+ PKG + SHR       S  +   I      L  LP++H          
Sbjct: 175 VQILYTSGTTSDPKGAMHSHRSLMTEYSSCLLHLDIKASDRCLAALPLYHSAQMHVFTMP 234

Query: 259 AAFCGTNICLRQV-TAKGVYSAIAKYGVTHFCAAPVVLNTIVNAPPEEAIIPLPHLVHVM 317
           A   G   CL    T + +   +    +  F A P V   ++    E+ +      V  +
Sbjct: 235 ALLAGAFSCLTDTPTPEEILRLLKTEQLNSFFAPPTVWIALLRH--EQFVEAQLRHVQKL 292

Query: 318 TAGAAPPPSVLFAMSEKGFKVAHTYGLSETYGPSTICAWKPEWDSLPPIKQARLNARQGV 377
             GA+  P  +    E G ++  + GL   YG S I    P    L P +        G 
Sbjct: 293 YYGASIMPEPI--ARELGARLPQS-GLYNCYGQSEIA---PLATVLTPEEHRERPTSCG- 345

Query: 378 RYIALEGLDVVDTKTMKPVPADGTTMGEIVMRGNAVMKGYLKNPKANEESFADGWFHSGD 437
           R ++     ++D  T +   A G   GE+V R   +M GY + P    E+FADGWFHSGD
Sbjct: 346 RPVSNVLTRIIDPSTGEEC-APGVA-GELVHRSPQLMVGYWEKPAETAEAFADGWFHSGD 403

Query: 438 LAVKHPDGYIEIKDRSKDIIISGGENISSLEVENTLYLHPAVLEVSVVARPDERWGESPC 497
           L  +   GYI I DR KDI+ +GG  ++S +VE  LY HP V EV+V+  PD++W E+  
Sbjct: 404 LGYRDAQGYIWIVDRIKDIVNTGGVLVASRDVEEALYRHPHVAEVAVIGVPDQKWIEAIA 463

Query: 498 AFVTLKPNIDKSNEQVLAEDIIKFCKSKMPAYWVPKSVVF-GPLPKTATGKIQKHVLRAK 556
           A V L     K N  + A+ ++   ++ +  + VPK V F   LPK ++GK+ K VLR  
Sbjct: 464 AVVVL-----KQNATLDAQALLHHARAHLAPFKVPKHVHFVEQLPKNSSGKLLKRVLRV- 517

Query: 557 AKEMGALKKSNL 568
             + GA  +S+L
Sbjct: 518 --QFGASARSSL 527


Lambda     K      H
   0.318    0.134    0.415 

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: 785
Number of extensions: 41
Number of successful extensions: 3
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: 568
Length of database: 542
Length adjustment: 36
Effective length of query: 532
Effective length of database: 506
Effective search space:   269192
Effective search space used:   269192
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 Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis