Aligments for a candidate for prpE in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Aligments for a candidate for prpE in Pseudomonas fluorescens FW300-N1B4

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate Pf1N1B4_2849 Acetyl-coenzyme A synthetase (EC 6.2.1.1)

Query= SwissProt::P27550
         (652 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2849
          Length = 645

 Score =  812 bits (2098), Expect = 0.0
 Identities = 379/629 (60%), Positives = 485/629 (77%), Gaps = 7/629 (1%)

Query: 19  INPQQYEAMYQQSINVPDTFWGEQG-KILDWIKPYQKVKNTSFAPGNVSIKWYEDGTLNL 77
           ++   Y+ +Y+QSI  P TFW EQ  + LDW  P+Q V+      G  S  W+  G +N+
Sbjct: 19  LSQDDYQRLYRQSIEHPSTFWAEQATRFLDWSAPWQTVQRYDLKTGEAS--WFAGGQINV 76

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

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

Query: 198 LKKNVDDALKN-PNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDLVEQASDQHQAEEMNAE 256
           LK+NVD AL++ PNV +V   +V++RT G+++W E RD+W+H  +   SD    E M+AE
Sbjct: 197 LKQNVDTALQSCPNVNTV---IVVERTQGQVNWVEDRDIWYHQALRDVSDDCPPEPMDAE 253

Query: 257 DPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTADVGWVTGHSYL 316
           DPLFILYTSGSTGKPKGV+HTTGGYL+ AA+TFKYVFDY  G+I+WCTADVGWVTGHSY+
Sbjct: 254 DPLFILYTSGSTGKPKGVMHTTGGYLLQAAMTFKYVFDYRDGEIFWCTADVGWVTGHSYI 313

Query: 317 LYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALMAEGDKAIEGTD 376
           +YGPLA GATTL+FEGVP++P+ +R  QV+DKH VNI YTAPTA+RALM EG + ++ T 
Sbjct: 314 VYGPLANGATTLIFEGVPSYPSTSRFWQVIDKHHVNIFYTAPTALRALMREGPEPLKETS 373

Query: 377 RSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITPLPGATELKAGS 436
           R SLR+LG+VGEPINPEAWEWY+  +G ++C +VDTWWQTETGG MI+PL     +K G 
Sbjct: 374 RESLRLLGTVGEPINPEAWEWYFNTVGEQRCTIVDTWWQTETGGIMISPLVSTQRVKPGC 433

Query: 437 ATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGDHERFEQTYFSTFKNMY 496
           AT+P FGVQP L+D  G  ++GA  G L I  SWP Q R+++GD +R  +TYF  +   Y
Sbjct: 434 ATQPMFGVQPVLLDEHGKEIKGAGSGILAIKSSWPAQIRSVYGDPKRMIETYFKPYPGYY 493

Query: 497 FSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAVVGIPHNIKG 556
           F+GDGARRDEDG YWITGR+DDV+NVSGHR+GTAE+ESALV H  IAEAAVVG PH++KG
Sbjct: 494 FTGDGARRDEDGDYWITGRIDDVINVSGHRIGTAEVESALVLHDSIAEAAVVGYPHDVKG 553

Query: 557 QAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTRSGKIMRRILR 616
           Q IYA+VT  +G EP+ EL  ++   V KEIG  A PD++ W  +LPKTRSGKIMRRILR
Sbjct: 554 QGIYAFVTPMNGTEPNDELKKQLLAHVSKEIGNFAKPDLIQWAPALPKTRSGKIMRRILR 613

Query: 617 KIAAGDTSNLGDTSTLADPGVVEKLLEEK 645
           KIA  +  +LGDTSTLADP VV+ L++++
Sbjct: 614 KIACNELDSLGDTSTLADPSVVQGLIDQR 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: 1397
Number of extensions: 52
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: 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 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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, or view the source code.

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