GapMind for Amino acid biosynthesis

 

Alignments for a candidate for prpE in Desulfatibacillum aliphaticivorans DSM 15576

Align 2-methylpropanoate--CoA ligase CCL4; HlCCL4; 2-methylbutanoate--CoA ligase CCL4; Butanoate--CoA ligase CCL3; Propionate--CoA ligase CCL3; EC 6.2.1.-; EC 6.2.1.17 (characterized)
to candidate WP_015949835.1 G491_RS0127745 long-chain-fatty-acid--CoA ligase

Query= SwissProt::M4IQQ5
         (556 letters)



>NCBI__GCF_000429905.1:WP_015949835.1
          Length = 555

 Score =  246 bits (628), Expect = 2e-69
 Identities = 187/564 (33%), Positives = 279/564 (49%), Gaps = 28/564 (4%)

Query: 1   MEDLKPRPASSS---PLTPLGFLERAATVYG--DCTSVVYDA--VSYTWSQTHRRCLCLA 53
           ME +K  PA+S    PL     ++ +   YG  +  S   D     YT+S  + R   LA
Sbjct: 1   MELIKGFPATSQDRYPLNVTNIIKHSVRNYGPQEIASRRLDGSMFRYTYSDAYERMQRLA 60

Query: 54  SSIASLGIENGHVVSVLAPNVPQMYELHFAVPMAGAILNAVNLRLDARTISILLHHSESK 113
           + +  LG++ G  V VLA N  + YE++F VP  GA++  +NLRL  + ++ ++ HS  +
Sbjct: 61  NGLTKLGVKVGDRVGVLAWNSNENYEVYFGVPGMGAVMLLLNLRLTPQDLAYVVEHSGCE 120

Query: 114 LIFVDHLSRDLILEAIALFPKQAPVPRLVFMADESESGNSSELGKEFFCSYKDLIDRGDP 173
            I VD     L+  A AL P    +   V +    +  +  E   E   SY++L+   DP
Sbjct: 121 YIIVDET---LLPIAHALAPLCPQIKGYVVITMPGKKMSDVETPLENTHSYEELLAESDP 177

Query: 174 DFKWVMPKSEWDPMILNYTSGTTSSPKGVVHCHRGIFIMTVDSLIDWGVPKQPVYLWTLP 233
            F W M + E       YT+GTT  PKGV + HR +++ ++   ++ G+  +      +P
Sbjct: 178 VFDWPMME-ETSAYAACYTTGTTGKPKGVYYSHRDVYLHSMCIGMNTGMNVKDTCCQIVP 236

Query: 234 MFHANGWSYPWGMAAVGGTNICLRKFDSEIIYDMIKR---HGVTHMCGAPVV----LNML 286
           MFHA GW  P     VG   I    +  E +  + K     GVT   GAP +    L  +
Sbjct: 237 MFHALGWGLPQAATLVGSRIILPGMYTLETLDSLSKLIVDEGVTMSAGAPAIFMPLLEYI 296

Query: 287 SNAPGSEPLKTTVQIMTAGAPPPSAVLFRT-ESLGFAVSHGYGLTETAGLVVS---CAWK 342
            N     P  T V++++    PP +++    +  G  + H YG TET  LV       W 
Sbjct: 297 RNLE-ERPDLTGVRLLSGATEPPVSMMKGFWDMTGAEIIHAYGATETTPLVTINRLMPWL 355

Query: 343 KEWNHLPATERARLKSRQGVGTVMQTKIDVVDPVTGAAVKRDGSTLGEVVLRGGSVMLGY 402
           +    L   ER  LK +QG   V    + VVD  T   V  DG T GE+++RG  +   Y
Sbjct: 356 E--TSLSEDERWNLKKKQGFA-VGGLDVKVVD-ATLKDVAHDGKTPGEILIRGPWITGAY 411

Query: 403 LKDPEGTAKSMTADGWFYTGDVGVMHPDGYLEIKDRSKDVIISGGENLSSVEVESILYSH 462
              P G+  S T DG++ +GDVG M  +GYL+I DR KDVI SGGE +SSV++E+ + SH
Sbjct: 412 HNAP-GSEASFTEDGFWRSGDVGTMDENGYLKITDRVKDVIKSGGEWISSVDMENEIISH 470

Query: 463 PDILEAAVVARPDEFWGETPCAFVSLKKGLTKKPTEKEIVEYCRSKLPRYMVPKTVVFKE 522
            D+L+AAVV      W E P A V L+     K    +I  +  +   ++ +P  V+F +
Sbjct: 471 NDVLDAAVVGVEHPKWQERPLALVVLRDDAKGKVNADDIRAHLSNVFAKWQLPDEVLFVD 530

Query: 523 ELPKTSTGKVQKFILRDMARGMGS 546
           E+PKTS GK  K ++R   + M S
Sbjct: 531 EIPKTSVGKTDKKVIRAEHKDMYS 554


Lambda     K      H
   0.319    0.135    0.412 

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: 774
Number of extensions: 42
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: 556
Length of database: 555
Length adjustment: 36
Effective length of query: 520
Effective length of database: 519
Effective search space:   269880
Effective search space used:   269880
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Jul 25 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:

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:

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:

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:

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