Alignments for a candidate for prpE in Flavobacterium glycines Gm-149

GapMind for Amino acid biosynthesis

Alignments for a candidate for prpE in Flavobacterium glycines Gm-149

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_066328597.1 BLR17_RS00555 acetate--CoA ligase

Query= SwissProt::P27550
         (652 letters)



>NCBI__GCF_900100165.1:WP_066328597.1
          Length = 635

 Score =  679 bits (1751), Expect = 0.0
 Identities = 345/633 (54%), Positives = 442/633 (69%), Gaps = 13/633 (2%)

Query: 20  NPQQYEAMYQQSINVPDTFWGE-QGKILDWIKPYQKVKNTSFAPGNVSIKWYEDGTLNLA 78
           N ++Y   Y++SI  P  FW +   +   W + + KV + + A     IKW+ D  +N+ 
Sbjct: 8   NFEEYFKEYKKSIKDPKKFWDKIASENFTWYQEWDKVVDFNMA--EAEIKWFVDAKVNIT 65

Query: 79  ANCLDRHLQENGDRTAIIWEG---DDASQSKHISYKELHRDVCRFANTLLELGIKKGDVV 135
            NC+DRHL + GD+TAII+E    D+ASQS   +Y ELH+ V + AN LL  GI+KGD V
Sbjct: 66  KNCIDRHLAKKGDKTAIIFEPNNPDEASQS--FTYNELHQKVSKMANVLLSQGIQKGDRV 123

Query: 136 AIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVITSDEGVRAGRS 195
            IY+PM+PE A+A LACARIGA+HSV+F GFS  AVA RI DS  ++VITSD G R  ++
Sbjct: 124 CIYLPMIPELAIATLACARIGAIHSVVFAGFSASAVAARINDSECKMVITSDGGYRGNKT 183

Query: 196 IPLKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDLVEQASDQHQAEEMNA 255
           I LK  VD+AL N    SVE V+V KRT   +  +EGRD W   LVE+ASD + AE M+A
Sbjct: 184 IDLKGIVDEALVN--CPSVEKVLVAKRTNTDVQMKEGRDQWLAPLVEKASDNNAAEIMDA 241

Query: 256 EDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTADVGWVTGHSY 315
           EDPLFILYTSGSTGKPKG++HTT GY+VY A TF+ VF+Y   D++WCTAD+GW+TGHSY
Sbjct: 242 EDPLFILYTSGSTGKPKGMVHTTAGYMVYTAYTFQNVFNYEENDVFWCTADIGWITGHSY 301

Query: 316 LLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALMAEGDKAIEGT 375
           +LYGPL  GATT++FEGVP++P  +R  +V++KH+VN  YTAPTAIRAL  E    ++  
Sbjct: 302 ILYGPLLNGATTVIFEGVPSYPDFSRFWEVIEKHKVNQFYTAPTAIRALAKESLDYVQKY 361

Query: 376 DRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITPLPGATELKAG 435
             SSL+++GSVGEPIN EAW WY   +G ++CPVVDTWWQTETGG +I+P+P  T  K  
Sbjct: 362 PLSSLKVIGSVGEPINEEAWHWYNDHVGGKRCPVVDTWWQTETGGILISPIPFITPTKPT 421

Query: 436 SATRPFFGVQPALVDNEGNPLE-GATEGSLVITDSWPGQARTLFGDHERFEQTYFSTFKN 494
            AT P  G+Q  L+D + N +E     GSL I   WPG ART++GDH+R+++TYFSTF  
Sbjct: 422 YATLPLPGIQAVLMDEKRNEIEDNQVVGSLCIKFPWPGIARTIWGDHKRYKETYFSTFPG 481

Query: 495 MYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAVVGIPHNI 554
            YFSGDGA RDE GYY ITGRVDDV+ VSGH LGTA IE A+  HP +AE+A+VG PH+I
Sbjct: 482 KYFSGDGALRDEVGYYRITGRVDDVIIVSGHNLGTAPIEDAINEHPAVAESAIVGFPHDI 541

Query: 555 KGQAIYAYVTLNHGEE--PSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTRSGKIMR 612
           KG A+Y +V L    E      L  E+   +   IGP+A  D + +   LPKTRSGKIMR
Sbjct: 542 KGNALYGFVILKETGEKRDKANLAKEINQHIADHIGPIAKLDKIQFVSGLPKTRSGKIMR 601

Query: 613 RILRKIAAGDTSNLGDTSTLADPGVVEKLLEEK 645
           RILRKIA GD SN GDT+TL +P +V+++   K
Sbjct: 602 RILRKIAEGDFSNFGDTTTLLNPEIVDEIKNGK 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: 1231
Number of extensions: 52
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 Jul 26 2024. The underlying query database was built on Jul 25 2024.

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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 2024 update 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
changes to Amino acid biosynthesis since the original publication.

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 Amino acid biosynthesis