Alignments for a candidate for prpE in Pedobacter arcticus A12

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpE in Pedobacter arcticus A12

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_017257106.1 B176_RS0102045 acetate--CoA ligase

Query= SwissProt::P27550
         (652 letters)



>NCBI__GCF_000302595.1:WP_017257106.1
          Length = 635

 Score =  698 bits (1801), Expect = 0.0
 Identities = 344/629 (54%), Positives = 435/629 (69%), Gaps = 10/629 (1%)

Query: 23  QYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSFAPGNVSIKWYEDGTLNLAANCL 82
           +Y+  YQ+S+  P+ FW +      W K + KV + +F      I+W++   LN+  NC+
Sbjct: 10  EYKEAYQRSVEQPEAFWADIADNFQWKKKWDKVLDWNFK--EPKIEWFKGAKLNITENCI 67

Query: 83  DRHLQENGDRTAIIWEGDDASQSKHI-SYKELHRDVCRFANTLLELGIKKGDVVAIYMPM 141
           DRHL + GD+ AIIWE +D ++   + +YK+LH  VC FAN L    +KKGD V IYMPM
Sbjct: 68  DRHLADKGDQPAIIWEANDPNEHHRVLTYKQLHEKVCLFANVLKNNDVKKGDRVCIYMPM 127

Query: 142 VPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVITSDEGVRAGRSIPLKKN 201
           +PE A+A+LACARIGA+HSV+FGGFS +++A RI D+   +VIT+D G R  + IPLK  
Sbjct: 128 IPELAIAVLACARIGAIHSVVFGGFSAQSIADRINDAQCEMVITADGGFRGPKDIPLKNV 187

Query: 202 VDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDLVEQASDQHQ----AEEMNAED 257
           +DDAL      SV+ V+VL RT   I   +GRD WW D + +          AEEM+AED
Sbjct: 188 IDDALVQ--CPSVKTVIVLTRTRTPISMIKGRDKWWQDEIHKVETLGMIDCPAEEMDAED 245

Query: 258 PLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTADVGWVTGHSYLL 317
           PLFILYTSGSTGKPKGV+HTT GY++Y A TF+ VF Y P D+Y+CTAD+GW+TGHSY++
Sbjct: 246 PLFILYTSGSTGKPKGVVHTTAGYMIYTAYTFQNVFQYQPQDVYFCTADIGWITGHSYII 305

Query: 318 YGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALMAEGDKAIEGTDR 377
           YGPLA GATTLMFEGVP +P   R   +VDK +VN LYTAPTAIR+LM  G   ++  D 
Sbjct: 306 YGPLAQGATTLMFEGVPTYPDAGRFWDIVDKFKVNTLYTAPTAIRSLMQSGLDYVKDKDL 365

Query: 378 SSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITPLPGATELKAGSA 437
           SSL++LGSVGEPIN EAW WY   IG  KCP+VDTWWQTE GG +I+P+   T  K   A
Sbjct: 366 SSLKVLGSVGEPINEEAWHWYNDNIGKGKCPIVDTWWQTENGGILISPIANVTPTKPCYA 425

Query: 438 TRPFFGVQPALVDNEGNPLEG-ATEGSLVITDSWPGQARTLFGDHERFEQTYFSTFKNMY 496
           T P  GVQP LVD  G  +EG    G+L I   WPG  RT +GDHER + TYFST+++MY
Sbjct: 426 TLPLPGVQPVLVDENGAVIEGNGVSGNLCIKFPWPGMLRTTYGDHERCKLTYFSTYEDMY 485

Query: 497 FSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAVVGIPHNIKG 556
           F+GDG  RDEDGYY ITGRVDDV+NVSGHR+GTAE+E+A+     + E+AVVG PH IKG
Sbjct: 486 FTGDGCLRDEDGYYRITGRVDDVINVSGHRIGTAEVENAINMFTDVVESAVVGYPHEIKG 545

Query: 557 QAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTRSGKIMRRILR 616
           Q IYAYV L+   E       ++   V + IG +A PD + +   LPKTRSGKIMRRILR
Sbjct: 546 QGIYAYVILDKESEDVELTKKDIAMTVSRIIGAIARPDKIQFVTGLPKTRSGKIMRRILR 605

Query: 617 KIAAGDTSNLGDTSTLADPGVVEKLLEEK 645
           KIA GD  N+GD STL DP VVE++++ K
Sbjct: 606 KIAEGDMKNVGDVSTLLDPAVVEEIIKGK 634


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: 1290
Number of extensions: 49
Number of successful extensions: 6
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: 635
Length adjustment: 38
Effective length of query: 614
Effective length of database: 597
Effective search space:   366558
Effective search space used:   366558
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