Alignments for a candidate for prpE in Chlorobium phaeobacteroides BS1

GapMind for Amino acid biosynthesis

Alignments for a candidate for prpE in Chlorobium phaeobacteroides BS1

Align acetate-CoA ligase (EC 6.2.1.1) (characterized)
to candidate 642683066 Cphamn1_0550 acetyl-coenzyme A synthetase (EC 6.2.1.1)

Query= BRENDA::Q9NR19
         (701 letters)



>IMG__ChlphaBS1_FD:642683066
          Length = 663

 Score =  696 bits (1797), Expect = 0.0
 Identities = 334/666 (50%), Positives = 465/666 (69%), Gaps = 35/666 (5%)

Query: 27  RSWSPPPEVSRSAHVPSLQRYRELHRRSVEEPREFWGDIAKEFYWKTPCPGPFLRYNFDV 86
           R + PPPE S +A + S+  Y +L+ ++ ++P ++WG IA+EF+W+        ++N  +
Sbjct: 26  RKFPPPPEFSENARISSMDEYEKLYAKAQKDPEKYWGGIAEEFHWEK-------KWNSVL 78

Query: 87  TKGKIFIEWMKGATTNICYNVLDRNVHEKKLGDKVAFYWEGNEPGETTQITYHQLLVQVC 146
                + +W  G TTN+CYN +DR+V   +  +K A  WEG E GE   +TY +L  QV 
Sbjct: 79  DWKPPYAKWFSGGTTNLCYNAVDRHVKSWRK-NKAAIIWEGEE-GEQRVLTYGELHRQVS 136

Query: 147 QFSNVLRKQGIQKGDRVAIYMPMIPELVVAMLACARIGALHSIVFAGFSSESLCERILDS 206
           +F+NVL+  G+Q GDRVAIYM M+PEL +A+LACAR+GA+H+++FAGFS+ ++ ER+ DS
Sbjct: 137 KFANVLKIAGVQPGDRVAIYMGMVPELAIAVLACARVGAVHNVIFAGFSAHAITERVNDS 196

Query: 207 SCSLLITTDAFYRGEKLVNLKELADEALQKCQEKGFPVRCCIVVKHLGRAELGMGDSTSQ 266
              L+I +D   R  K +NLK++ DEA+         VR  IV+K           +T++
Sbjct: 197 RAKLIICSDGTRRRGKTINLKDIVDEAIVNTPS----VRSVIVLK-----------TTNE 241

Query: 267 SPPIKRSCPDVQISWNQGIDLWWHELMQEAGDECEPEWCDAEDPLFILYTSGSTGKPKGV 326
                      ++  + G+D WWH+LM  A D  +PE+ DAE PLFILYTSGSTGKPKG+
Sbjct: 242 -----------EVHMHDGMDHWWHDLMGLAVDHNDPEFVDAEHPLFILYTSGSTGKPKGI 290

Query: 327 VHTVGGYMLYVATTFKYVFDFHAEDVFWCTADIGWITGHSYVTYGPLANGATSVLFEGIP 386
           +HT GGYM++ A +FK+VFD   ED++WCTAD+GWITGH+Y+ YGPL NGAT +++EG P
Sbjct: 291 LHTTGGYMVHAANSFKHVFDIKDEDIYWCTADVGWITGHTYLVYGPLLNGATIMMYEGAP 350

Query: 387 TYPDVNRLWSIVDKYKVTKFYTAPTAIRLLMKFGDEPVTKHSRASLQVLGTVGEPINPEA 446
            YP  +R W I++++KVT  YTAPTAIR  ++ GDE VTKH  +SL++LGTVGEPINP+A
Sbjct: 351 NYPQWDRFWDIINRHKVTILYTAPTAIRAFIRAGDEWVTKHDLSSLRLLGTVGEPINPKA 410

Query: 447 WLWYHRVVGAQRCPIVDTFWQTETGGHMLTPLPGATPMKPGSATFPFFGVAPAILNESGE 506
           W+WYH V+G ++CPIVDT+WQTETGG +++PLPGATP KPG+AT P  G+   +L + G+
Sbjct: 411 WMWYHTVIGKEKCPIVDTWWQTETGGILVSPLPGATPTKPGTATRPLPGIMVDVLRKDGK 470

Query: 507 ELEGEAEGYLVFKQPWPGIMRTVYGNHERFETTYFKKFPGYYVTGDGCQRDQDGYYWITG 566
             +    GYLV KQPWP ++RT+YG+++R+E TY+ +F   Y TGDG ++D+DGY WI G
Sbjct: 471 PCKPNEGGYLVIKQPWPSMLRTIYGDNKRYEDTYWSEFKDIYFTGDGARKDEDGYIWIMG 530

Query: 567 RIDDMLNVSGHLLSTAEVESALVEHEAVAEAAVVGHPHPVKGECLYCFVTLCDGHTFSPK 626
           R+DD++NVSGH L T+EVESALV HEAVAEAAVV  P  +KG  L  FVTL D +    K
Sbjct: 531 RVDDVVNVSGHRLGTSEVESALVAHEAVAEAAVVSRPDEIKGNSLIAFVTLKDEYVGDMK 590

Query: 627 LTEELKKQIREKIGPIATPDYIQNAPGLPKTRSGKIMRRVLRKIAQNDHDLGDMSTVADP 686
           L ++L+  + ++IGPIA PD I+ A GLPKTRSGKIMRR+LR++A      GD++T+ D 
Sbjct: 591 LRDDLRGHVAKEIGPIAKPDEIRWAQGLPKTRSGKIMRRLLRELASTKEIKGDVTTLEDF 650

Query: 687 SVISHL 692
            V+  L
Sbjct: 651 GVLEQL 656


Lambda     K      H
   0.320    0.138    0.440 

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: 1334
Number of extensions: 60
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: 701
Length of database: 663
Length adjustment: 39
Effective length of query: 662
Effective length of database: 624
Effective search space:   413088
Effective search space used:   413088
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 (21.8 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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