Alignments for a candidate for prpE in Erythrobacter gangjinensis K7-2

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpE in Erythrobacter gangjinensis K7-2

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_047005978.1 AAW01_RS03860 acetate--CoA ligase

Query= SwissProt::P27550
         (652 letters)



>NCBI__GCF_001010925.1:WP_047005978.1
          Length = 642

 Score =  833 bits (2152), Expect = 0.0
 Identities = 397/628 (63%), Positives = 492/628 (78%), Gaps = 7/628 (1%)

Query: 21  PQQYEAMYQQSINVPDTFWGEQGKI-LDWIKPYQKVKNTSFAPGNVSIKWYEDGTLNLAA 79
           P+QY+A+Y++S+  PD FW EQ K  LDW     K    S+ P  V IKW+ DGTLN+  
Sbjct: 18  PEQYDALYERSVQDPDGFWLEQAKERLDWYTAPTKGAEWSYDP--VDIKWFSDGTLNICY 75

Query: 80  NCLDRHLQENGDRTAIIWEGDDA-SQSKHISYKELHRDVCRFANTLLELGIKKGDVVAIY 138
           N +DRHL  +GD+ A+I+E D   +  + ++Y++LH++V R AN L  +G++KGD V +Y
Sbjct: 76  NAVDRHLDTHGDQIALIFEPDSPDAPGRSLTYRQLHKEVTRVANALKAMGVRKGDRVTLY 135

Query: 139 MPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVITSDEGVRAGRSIPL 198
           MPM+ E A+ MLACARIGA+HSV+FGGFSPEA+AGRI+   SR V+ +D+G+R  +++PL
Sbjct: 136 MPMIVEGALTMLACARIGAIHSVVFGGFSPEALAGRIMACESRFVVCADQGLRGSKTVPL 195

Query: 199 KKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDLVEQASDQHQAEEMNAEDP 258
           K NVD AL    V SV+ V+V   TGG+I+  +GRD W+ D    + D+   EEMNAEDP
Sbjct: 196 KANVDAALAMQGV-SVDGVLVFDHTGGEIEMVDGRDHWFADFA--SDDECPCEEMNAEDP 252

Query: 259 LFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTADVGWVTGHSYLLY 318
           LFILYTSGSTG PKGVLHTTGGY ++AA TF Y FDY PGDI+WC+AD+GWVTGH+Y+ Y
Sbjct: 253 LFILYTSGSTGTPKGVLHTTGGYALWAATTFHYTFDYQPGDIFWCSADIGWVTGHTYVTY 312

Query: 319 GPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALMAEGDKAIEGTDRS 378
           GPL    T+L+FEGVPN+P   R   V+DKH+VN+ YTAPTAIRALM EGD  +   + S
Sbjct: 313 GPLINAGTSLIFEGVPNYPDHGRFWDVIDKHKVNLFYTAPTAIRALMREGDSFVTSRNLS 372

Query: 379 SLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITPLPGATELKAGSAT 438
           SLR+LG+VGEPINPEAW WY++ +G + CP+VDTWWQTETGG MIT LP A ++K GSA 
Sbjct: 373 SLRVLGTVGEPINPEAWRWYYEVVGKKNCPIVDTWWQTETGGHMITTLPYAHDMKPGSAG 432

Query: 439 RPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGDHERFEQTYFSTFKNMYFS 498
           +PFFG+QP LVDN+GN LEGATEG+L IT SWPGQART++GDH+RFEQ YFST+   YF+
Sbjct: 433 KPFFGIQPLLVDNDGNTLEGATEGNLCITHSWPGQARTVYGDHDRFEQAYFSTYPGRYFT 492

Query: 499 GDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAVVGIPHNIKGQA 558
           GDG RRDEDGYYWITGRVDDV+NVSGHR+GTAE+ESALV HPK+AEAAVVG PH+IKGQ 
Sbjct: 493 GDGCRRDEDGYYWITGRVDDVINVSGHRMGTAEVESALVLHPKVAEAAVVGYPHDIKGQG 552

Query: 559 IYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTRSGKIMRRILRKI 618
           IY YVTLN GEE S ELY+E+R  VRKEIGP+ATPD L +TD LPKTRSGKIMRRILRKI
Sbjct: 553 IYCYVTLNAGEEGSDELYSELRQHVRKEIGPIATPDHLQFTDGLPKTRSGKIMRRILRKI 612

Query: 619 AAGDTSNLGDTSTLADPGVVEKLLEEKQ 646
           A  D  +LGDTSTLADP +V++L+E +Q
Sbjct: 613 AENDYGSLGDTSTLADPSLVDRLIEGRQ 640


Lambda     K      H
   0.317    0.135    0.421 

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: 1485
Number of extensions: 72
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: 652
Length of database: 642
Length adjustment: 38
Effective length of query: 614
Effective length of database: 604
Effective search space:   370856
Effective search space used:   370856
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: 54 (25.4 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
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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

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 catabolism of small carbon sources