GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Halioglobus japonicus S1-36

Align Fatty acid oxidation complex subunit alpha; EC 4.2.1.17; EC 5.1.2.3; EC 5.3.3.8; EC 1.1.1.35 (characterized)
to candidate WP_084199858.1 C0029_RS05645 3-hydroxyacyl-CoA dehydrogenase

Query= SwissProt::P21177
         (729 letters)



>NCBI__GCF_002869505.1:WP_084199858.1
          Length = 715

 Score =  348 bits (893), Expect = e-100
 Identities = 233/712 (32%), Positives = 368/712 (51%), Gaps = 25/712 (3%)

Query: 15  DGIAELVFDAPGSVNKLDTATVASLGEAIGVLEQQSDLKGLLLRSNKAAFIVGADITEFL 74
           DGI  +  D  G VN ++      +G+ I  L+++  L G++L S K  F  G ++ + L
Sbjct: 11  DGIVTVTMDMNGPVNSMNEEYRQLMGDTITRLQEEEGLTGVVLASAKKVFFAGGNLYDLL 70

Query: 75  SLFLVPEEQLSQWLHFANSVFNRLEDLPVPTIAAVNGYALGGGCECVLATDYRLATPD-- 132
           +       Q  Q L         LE LPVP +AA+NG ALGGG E  LA ++R+A  +  
Sbjct: 71  AAREEDIPQFMQELDLTKGQLRALEKLPVPVVAAINGAALGGGFEICLACNHRIAWDNRA 130

Query: 133 LRIGLPETKLGIMPGFGGSVRMPRMLGADSALEIIAAGKDVGADQALKIGLV-DGVVKAE 191
           +++GLPE  LG++PG GG VRM  +LG  +AL  +  G  V  ++AL  G++ + V   +
Sbjct: 131 VQLGLPEVSLGLLPGGGGVVRMVNLLGLQAALPYLLEGTRVSPEKALAAGMIHETVASVD 190

Query: 192 KLVEGAKAVLRQAINGDL----DWKAKRQPKLEPLKLSKIEATMSFTIAKGMVAQTAGKH 247
           +LV  AKA + +  + +      W  K   K+     +        T A  M+ Q     
Sbjct: 191 ELVPRAKAWILENKDNEAAAVQPWDVKGH-KIPGGNAAHPANAQMITAAPAMLFQKTRGL 249

Query: 248 YPAPITAVKTIEAAARFGREEALNLENKSFVPLAHTNEARALVG-IFLNDQYVKGKAKKL 306
            PAPI  +     AAR   + AL +E++    LA T EA+  +   F     V G A + 
Sbjct: 250 LPAPIKILDCAVEAARLNLDTALVVESRGLAELAITPEAKNQISTFFFGMNKVNGGASR- 308

Query: 307 TKDVETPK--QAAVLGAGIMGGGIAYQSAWKGVPVVMKDINDKSLTLGMTEAAKLLNKQL 364
            +D+E  K  +  VLGAG+MG GIAY SA  G+ VV+KDI+ ++   G   +  LL K++
Sbjct: 309 PQDIEPQKTTKVGVLGAGMMGQGIAYVSAMAGIEVVLKDISQEAADQGKAYSETLLAKRV 368

Query: 365 ERGKIDGLKLAGVISTIHPTLDYAGFDRVDIVVEAVVENPKVKKAVLAETEQKVRQDTVL 424
            +G++D  K   +++ I PT + A     D+V+EAV EN ++K  +  + +  + +D + 
Sbjct: 369 AKGRMDQAKADAILALIKPTAEDADLQGCDLVIEAVFENMELKHTITKDLQGYMAEDGIW 428

Query: 425 ASNTSTIPISELANALERPENFCGMHFFNPVHRMPLVEIIRGEKSSDETIAKVVAWASKM 484
            SNTST+PI++LA    +PENF G+HFF+PV +MPLVEII GE++ D T+AK   +  ++
Sbjct: 429 GSNTSTLPITQLAEVATKPENFIGIHFFSPVDKMPLVEIICGEQTGDVTLAKAFDYCKQI 488

Query: 485 GKTPIVVNDCPGFFVNRVLFPYFAGFSQLLRDGADFRKIDKVMEKQFGWPMGPAYLLDVV 544
            KTPIVVND  GFF +R    Y     QLL DG    ++D  + K  G P+GP  + D V
Sbjct: 489 RKTPIVVNDSLGFFTSRTFGTYLDEGMQLLVDGVHPIQVDN-LGKAIGMPVGPLQVHDEV 547

Query: 545 GIDTAHHAQAVMA--AGFPQRMQKDYRDAIDALF--DANRFGQKNGLGFWRYKEDSKGKP 600
            ++    A    A      Q        A+ A    D  R G+ +G GF+ Y  D     
Sbjct: 548 SLELTKKAGQTHADLGVLDQWGDGSVGRAVIATMVDDHGRGGRHHGGGFYEYAADG---- 603

Query: 601 KKEEDAAVEDLLAEVSQPKRDFSEEEIIARMMIPMVNEVVRCLEEGIIATPAEADMALVY 660
                +    LL    +P+ D   ++I  R++   V E ++CLE G++ + A+ ++  + 
Sbjct: 604 ---SRSLWPTLLDLYHKPETDLPAQDIKDRLLFRQVIESLKCLEGGVLRSVADGNIGSIM 660

Query: 661 GLGFPPFHGGAFRWLDTLGSAKYLDMAQQYQ-HLGPLYEVPEGLRNKARHNE 711
           G+G P + GG  ++++T G  +++D   + +   G  ++ P  + +K    E
Sbjct: 661 GIGAPVWTGGFIQFVNTYGLQRFIDRCAELEAAYGERFKAPAIVADKLAAGE 712


Lambda     K      H
   0.318    0.136    0.399 

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: 1194
Number of extensions: 76
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: 729
Length of database: 715
Length adjustment: 40
Effective length of query: 689
Effective length of database: 675
Effective search space:   465075
Effective search space used:   465075
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: 55 (25.8 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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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