Alignments for a candidate for prpE in Pseudomonas baetica a390

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpE in Pseudomonas baetica a390

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_100847194.1 C0J26_RS06710 acetate--CoA ligase

Query= SwissProt::P27550
         (652 letters)



>NCBI__GCF_003031005.1:WP_100847194.1
          Length = 645

 Score =  821 bits (2120), Expect = 0.0
 Identities = 382/628 (60%), Positives = 482/628 (76%), Gaps = 5/628 (0%)

Query: 19  INPQQYEAMYQQSINVPDTFWGEQG-KILDWIKPYQKVKNTSFAPGNVSIKWYEDGTLNL 77
           ++   Y+ +Y++SI  P  FW EQ  + LDW  P+Q V+      G  +  W+  G LN+
Sbjct: 19  LSQDDYQRLYRESIEHPSAFWAEQALRFLDWSTPWQTVQRYDLKAGEAA--WFAGGKLNV 76

Query: 78  AANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCRFANTLLELGIKKGDVVAI 137
           + NC+DRHL++ GD+TA++WEGDD ++S  I+YK+LH  VCR AN L   G+KKGD V I
Sbjct: 77  SYNCIDRHLEQRGDQTALLWEGDDPAESAQITYKKLHHHVCRLANVLKSRGVKKGDRVCI 136

Query: 138 YMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVITSDEGVRAGRSIP 197
           YMPM+PEA  AMLACARIGA+HSV+FGGFSP+++  RI+D++ R VIT+DEGVR G+ +P
Sbjct: 137 YMPMIPEAVYAMLACARIGAIHSVVFGGFSPDSLRDRILDADCRTVITADEGVRGGKFVP 196

Query: 198 LKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDLVEQASDQHQAEEMNAED 257
           LK+NVD AL+N    +V  VVV++RT G +DW EGRDLW+H  V   SD    E M+AED
Sbjct: 197 LKQNVDKALQN--CPAVSTVVVVERTQGNVDWVEGRDLWYHQAVRDVSDDCPPEPMDAED 254

Query: 258 PLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTADVGWVTGHSYLL 317
           PLFILYTSGSTGKPKGVLHTTGGYL+ AA+TFKYV DY  G+++WCTADVGWVTGHSY++
Sbjct: 255 PLFILYTSGSTGKPKGVLHTTGGYLLQAAMTFKYVLDYRDGEVFWCTADVGWVTGHSYIV 314

Query: 318 YGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALMAEGDKAIEGTDR 377
           YGPLA GATTLMFEGVP++P  +R  QV+DKH+VNI YTAPTA+RALM EG + ++ T R
Sbjct: 315 YGPLANGATTLMFEGVPSYPNSSRFWQVIDKHKVNIFYTAPTALRALMREGAEPLKETSR 374

Query: 378 SSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITPLPGATELKAGSA 437
            SLR+LGSVGEPINPEAWEWY+  +G ++CP+VDTWWQTETGG M++PL  A  +K G A
Sbjct: 375 QSLRLLGSVGEPINPEAWEWYFNVVGEQRCPIVDTWWQTETGGIMLSPLVSAQRIKPGCA 434

Query: 438 TRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGDHERFEQTYFSTFKNMYF 497
           T+P FGVQP L+D +G  ++GA  G L I  SWP Q R+++GD +R   TYF  +   YF
Sbjct: 435 TQPMFGVQPVLLDEQGKEIKGAGSGVLAIKSSWPAQIRSVYGDPQRMVDTYFKPYPGYYF 494

Query: 498 SGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAVVGIPHNIKGQ 557
           +GDGARRDEDG YWITGR+DDV+NVSGHR+GTAE+ESALV H  IAEAAVVG PH++KGQ
Sbjct: 495 TGDGARRDEDGDYWITGRIDDVINVSGHRIGTAEVESALVLHDSIAEAAVVGYPHDVKGQ 554

Query: 558 AIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTRSGKIMRRILRK 617
            IYA+VT  +G EP+ EL  E+   V KEIG  A PD++ W  +LPKTRSGKIMRRILRK
Sbjct: 555 GIYAFVTPMNGTEPNDELKKELLAHVSKEIGSFAKPDLIQWAPALPKTRSGKIMRRILRK 614

Query: 618 IAAGDTSNLGDTSTLADPGVVEKLLEEK 645
           IA  +  +LGDTSTLADP VV+ L++++
Sbjct: 615 IACNELDSLGDTSTLADPSVVQGLIDKR 642


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: 1416
Number of extensions: 56
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: 652
Length of database: 645
Length adjustment: 38
Effective length of query: 614
Effective length of database: 607
Effective search space:   372698
Effective search space used:   372698
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)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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