GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Paraburkholderia bryophila 376MFSha3.1

Align 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate H281DRAFT_00916 H281DRAFT_00916 short chain enoyl-CoA hydratase /3-hydroxyacyl-CoA dehydrogenase

Query= reanno::BFirm:BPHYT_RS13545
         (706 letters)



>FitnessBrowser__Burk376:H281DRAFT_00916
          Length = 694

 Score =  596 bits (1537), Expect = e-174
 Identities = 317/686 (46%), Positives = 435/686 (63%), Gaps = 8/686 (1%)

Query: 18  VLLVTIDHAPVNALSADVRRGLLAAIEAADADKAVEAVLIVGAGRNFIAGADIREFGKPP 77
           V ++T+++ PVN L    R G++  IE A  D A++A+++ GAG+ F  GADI EF  P 
Sbjct: 11  VAVITLNNPPVNGLGLSTRAGIVEGIERAQNDAAIKAIVLTGAGKAFSGGADITEFNTPK 70

Query: 78  VP--PSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRIAVDGAKLGLPEVQLGL 135
               P+L  V   +E   KPVVAAIH  A+GGGLE+AL AHYRIA  GA++ LPEV+LG+
Sbjct: 71  ATQEPTLATVIKTVEGSPKPVVAAIHSVAMGGGLELALGAHYRIAAPGAQIALPEVKLGI 130

Query: 136 LPGAGGTQRTPRLIGAQAALDLILSGRHASAKEALAFGLIDRLGSSDDILAEGLAYVHEL 195
           LPGAGGTQR PR IG +AAL++I+SG    +++    GL D L   D +    LA+  ++
Sbjct: 131 LPGAGGTQRLPRAIGLEAALNMIVSGAPVMSQDLARSGLFDELADGD-LTEAALAFARKV 189

Query: 196 LAAHAPVRRTRDAAALSDRAASLAAVATARAETAKKSRGLFSPLKIVDAVEAAIEQPFDE 255
            A   P  + R+       A     +  AR   A  ++   +PLK +DAVEA ++  FD+
Sbjct: 190 GAKEGPHPKVRERKIEHPNAEGF--IQFARNSVATVAKNFPAPLKCIDAVEAGVKNGFDK 247

Query: 256 GLRVERKLFLECIDSPQRAGLIHAFFAEREVLKAPETRAAKP-RTLNTIGVVGGGTMGAG 314
           GL VER+ F+  + +P+   L HAFF ER   K P+  A  P R +  + V+G GTMG G
Sbjct: 248 GLAVERECFVALVQTPESRALRHAFFGERAASKIPDVPADTPVREIRQVAVIGAGTMGGG 307

Query: 315 IAVAVLDAGLPVTMIERDDASLARGRAHIEKVYDGLIAKGRLSAEKKAALMSRWSGSTSY 374
           IA+  + AG+PVT++E    +L RG A I K Y+  + KG+L  E     M+  + + SY
Sbjct: 308 IAMNFISAGIPVTLLETKQEALDRGLATIRKNYEATVKKGKLKPEALEERMALITPTLSY 367

Query: 375 DALAGADLVIEAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYLDIDALASSVSRPADVI 434
           D L  ADL++EAVFE+L VK+ VF  LD V K+GA+LA+NTS LD+D +A+   RP DV+
Sbjct: 368 DDLKNADLIVEAVFEELGVKEQVFKRLDEVAKSGAILASNTSTLDVDKIAAFTRRPQDVV 427

Query: 435 GLHFFSPANIMKLLEVVVPKQVSADVVATAFELAKKLRKTPVRAGVCDGFIGNRVLAVYR 494
           G+HFFSPAN+MKLLEVV  K+ + DV+AT  +LAKK++KT V +GVCDGFIGNR++  Y 
Sbjct: 428 GMHFFSPANVMKLLEVVRGKETAKDVLATVMKLAKKIKKTAVVSGVCDGFIGNRMIEQYI 487

Query: 495 SAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARKRRAATRNPAARYVQ 554
             A  M+++GA P Q+D A+  FGF MGPF++ DLAG DIGWA RKRR    +P   Y +
Sbjct: 488 RQALFMLDEGALPAQVDRAIEKFGFAMGPFRMSDLAGNDIGWAIRKRR-YEEHPEMHYSK 546

Query: 555 IADRLCERGWFGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAERARAGITPRSFTDEEIIR 614
           IADRLCE G FGQK+G G+Y Y  G R+  P   V+ +I A         R   D+EI+ 
Sbjct: 547 IADRLCETGRFGQKTGGGWYDYKAGDRTAHPSKLVDDMIVAYSNETNTQRRKIGDDEIVE 606

Query: 615 RYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYADMVGLPKILADIRE 674
           R + A++NEGA ++ E IA +P D+D+ +L GYGFP YRGGPM YAD VGL  +   IR 
Sbjct: 607 RLVFALVNEGAKILEEGIASKPSDIDMVYLTGYGFPLYRGGPMLYADTVGLYNVERAIRR 666

Query: 675 FAKE-DPLFWKPSPLLIELVERGADF 699
           +A + +   W+ +P + EL  +G  F
Sbjct: 667 YASQPNGDAWQLAPSIAELAAQGRGF 692


Lambda     K      H
   0.320    0.136    0.392 

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: 1082
Number of extensions: 54
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: 706
Length of database: 694
Length adjustment: 39
Effective length of query: 667
Effective length of database: 655
Effective search space:   436885
Effective search space used:   436885
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 (21.8 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Sep 17 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