Alignments for a candidate for prpE in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpE in Pseudomonas stutzeri RCH2

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate GFF2607 Psest_2657 acetate--CoA ligase

Query= SwissProt::P27550
         (652 letters)



>FitnessBrowser__psRCH2:GFF2607
          Length = 651

 Score =  912 bits (2357), Expect = 0.0
 Identities = 424/642 (66%), Positives = 517/642 (80%)

Query: 7   HTIPANIADRCLINPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSFAPGNVS 66
           + +    A   L +   Y AMYQQS+  P+ FW EQ   L+WI+P+ +VK TSF   +V 
Sbjct: 7   YPVSPEAAKHSLTDEAAYRAMYQQSVINPEGFWREQAARLNWIRPFTEVKRTSFDDHHVD 66

Query: 67  IKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCRFANTLLE 126
           IKW+ DGTLN++ANCLDRHL E GD+ AIIWEGD+ S+ + I+Y+EL+++VC+FAN L  
Sbjct: 67  IKWFADGTLNVSANCLDRHLAERGDQVAIIWEGDEPSEHREITYRELYQEVCKFANALRG 126

Query: 127 LGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVITS 186
             + +GDVV IYMPM+PEAAVAMLACARIGA+HSV+FGGFSPEA+AGRIID  S++VIT+
Sbjct: 127 QDVHRGDVVTIYMPMIPEAAVAMLACARIGAIHSVVFGGFSPEALAGRIIDGQSKVVITA 186

Query: 187 DEGVRAGRSIPLKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDLVEQASD 246
           DEG+R G+ IPLK+NVD+AL +P    V+ ++V++RTG  I W   RD+ + DL+  A +
Sbjct: 187 DEGIRGGKPIPLKENVDEALTHPQTRCVQKIIVVRRTGADIRWHPHRDVCYDDLMRVAGE 246

Query: 247 QHQAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTAD 306
               +EM AE+PLFILYTSGSTGKPKGVLHT GGYL+YAALT + VFDY PGD+YWCTAD
Sbjct: 247 VCAPKEMGAEEPLFILYTSGSTGKPKGVLHTCGGYLLYAALTHERVFDYRPGDVYWCTAD 306

Query: 307 VGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALMA 366
           +GW+TGHSYL+YGPLA GATTLM+EGVPN+P   R+A+++DKH+VNILYTAPTAIRA+MA
Sbjct: 307 IGWITGHSYLIYGPLANGATTLMYEGVPNYPDVTRIARIIDKHRVNILYTAPTAIRAMMA 366

Query: 367 EGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITPL 426
           EG  A+EG D SSLR+LG+VGEPINPEAW WY++ +G  +CP+VDTWWQTETGG +I+PL
Sbjct: 367 EGAAAMEGADGSSLRLLGTVGEPINPEAWHWYYETVGRSRCPIVDTWWQTETGGILISPL 426

Query: 427 PGATELKAGSATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGDHERFEQ 486
           PGAT LK GSATRP FGV P LVDN GN LEG  EG+LVI DSWPGQ RT++ DH+RF  
Sbjct: 427 PGATALKPGSATRPLFGVVPGLVDNLGNLLEGPAEGNLVILDSWPGQMRTIYRDHDRFVD 486

Query: 487 TYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAA 546
           TYF TF+ MYF+GDGARRDEDGYYWITGRVDDVLNVSGHR+GTAEIESA+VAH K+AEAA
Sbjct: 487 TYFKTFRGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHAKVAEAA 546

Query: 547 VVGIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTR 606
            VG+PH +KGQAIY YVTL  G EPS  L  E++ WVR EIGP+A PD + W   LPKTR
Sbjct: 547 AVGVPHALKGQAIYVYVTLVAGVEPSDTLRQELQQWVRHEIGPIAVPDTIQWAPGLPKTR 606

Query: 607 SGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEKQAI 648
           SGKIMRR+LRKIA  D   LGDTSTLADPGVV++L+E  +A+
Sbjct: 607 SGKIMRRLLRKIATDDYDALGDTSTLADPGVVDQLIEAHEAV 648


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: 1529
Number of extensions: 65
Number of successful extensions: 1
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: 651
Length adjustment: 38
Effective length of query: 614
Effective length of database: 613
Effective search space:   376382
Effective search space used:   376382
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 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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