Alignments for a candidate for prpE in Chryseobacterium angstadtii KM

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpE in Chryseobacterium angstadtii KM

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_048507311.1 ACM46_RS14065 acetate--CoA ligase

Query= SwissProt::P27550
         (652 letters)



>NCBI__GCF_001045465.1:WP_048507311.1
          Length = 636

 Score =  670 bits (1729), Expect = 0.0
 Identities = 337/630 (53%), Positives = 438/630 (69%), Gaps = 15/630 (2%)

Query: 24  YEAMYQQSINVPDTFWGEQGKILD----WIKPYQKVKNTSFAPGNVSIKWYEDGTLNLAA 79
           Y   Y++SI  P  FW    KI D    W + + KV    +      I W+++  LN+  
Sbjct: 12  YFEEYKKSIKNPKKFWD---KIADQNFVWYQRWSKV--VKYDMNEAKITWFKNAKLNITK 66

Query: 80  NCLDRHLQENGDRTAIIWEGDDASQ-SKHISYKELHRDVCRFANTLLELGIKKGDVVAIY 138
           NC+DRHL   G++TAIIWE +D  + ++HISY +L+  V + AN L E+GI+KGD V IY
Sbjct: 67  NCIDRHLAVRGEKTAIIWEPNDPKEEAQHISYNDLYTRVNKTANVLREMGIEKGDRVCIY 126

Query: 139 MPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVITSDEGVRAGRSIPL 198
           +PM+PE A+ MLACA++GAVHSVIF GFS  AVA R+ D +++++ITSD   R  + + L
Sbjct: 127 LPMIPELAITMLACAKLGAVHSVIFAGFSASAVASRVNDCHAKMIITSDGSYRGNKVLDL 186

Query: 199 KKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDLVEQASDQHQAEEMNAEDP 258
           K  VD+AL+     SVE V+V+KRT  +I  +EGRD W  DL E+AS       M+AEDP
Sbjct: 187 KSIVDEALEK--TPSVESVLVVKRTHNEIKMKEGRDYWMADLYEKASADFVTVIMDAEDP 244

Query: 259 LFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTADVGWVTGHSYLLY 318
           LFILYTSGSTGKPKG+LHT  GY+VY A TFK VF+Y   DIYWCTAD+GW+TGHSY+LY
Sbjct: 245 LFILYTSGSTGKPKGMLHTCAGYMVYTAYTFKNVFNYKENDIYWCTADIGWITGHSYILY 304

Query: 319 GPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALMAEGDKAIEGTDRS 378
           GPL  GATT++FEGVP +P P R  +V++KH++   YTAPTAIR+L  E  + ++  D S
Sbjct: 305 GPLLNGATTVIFEGVPTYPEPDRFWEVIEKHKITQFYTAPTAIRSLAKESTEWVDKHDLS 364

Query: 379 SLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITPLPGATELKAGSAT 438
           +L+++GSVGEPIN EAW W+   +G +KCPVVDTWWQTETGG MI+PLP  T  K   AT
Sbjct: 365 TLKVIGSVGEPINEEAWHWFNDHVGKKKCPVVDTWWQTETGGIMISPLPFVTPTKPTYAT 424

Query: 439 RPFFGVQPALVDNEGNPLEG-ATEGSLVITDSWPGQARTLFGDHERFEQTYFSTFKNMYF 497
            P  G+QP L+D++ N + G    G+L I   WPG ART++GDH+R+++TYFS F   YF
Sbjct: 425 LPLPGIQPVLMDDKRNEITGNQVTGNLCIRFPWPGIARTIWGDHQRYKETYFSAFPGKYF 484

Query: 498 SGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAVVGIPHNIKGQ 557
           +GDGA RDE GYY ITGRVDDV+ VSGH LGTA IE ++  HP +AE+A+VG PH+IKG 
Sbjct: 485 TGDGALRDEVGYYRITGRVDDVIIVSGHNLGTAPIEDSINEHPAVAESAIVGYPHDIKGN 544

Query: 558 AIYAYVTLNH-GEEPSPE-LYAEVRNWVRKEIGPLATPDVLHWTDSLPKTRSGKIMRRIL 615
           A+Y +V L   GE    E L  E+   +  +IGP+A  D + +   LPKTRSGKIMRRIL
Sbjct: 545 ALYGFVILKETGEGRDKENLKKEINQLISDQIGPIAKLDKIQFVSGLPKTRSGKIMRRIL 604

Query: 616 RKIAAGDTSNLGDTSTLADPGVVEKLLEEK 645
           RKIA GD SN GD STL +P +VE++  E+
Sbjct: 605 RKIAEGDFSNFGDISTLLNPEIVEEIKNER 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: 1287
Number of extensions: 62
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: 636
Length adjustment: 38
Effective length of query: 614
Effective length of database: 598
Effective search space:   367172
Effective search space used:   367172
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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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
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