GapMind for catabolism of small carbon sources

 

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

Align 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate H281DRAFT_00361 H281DRAFT_00361 short chain enoyl-CoA hydratase /3-hydroxyacyl-CoA dehydrogenase

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



>lcl|FitnessBrowser__Burk376:H281DRAFT_00361 H281DRAFT_00361 short
           chain enoyl-CoA hydratase /3-hydroxyacyl-CoA
           dehydrogenase
          Length = 706

 Score = 1280 bits (3311), Expect = 0.0
 Identities = 648/705 (91%), Positives = 682/705 (96%)

Query: 1   MTPNPSADVVSRELRGKVLLVTIDHAPVNALSADVRRGLLAAIEAADADKAVEAVLIVGA 60
           M+   S DVV+RELRGKVLLVTIDHAPVNALSADVRRGLLAAIEAAD+D +V+AVLIVGA
Sbjct: 1   MSLTTSTDVVTRELRGKVLLVTIDHAPVNALSADVRRGLLAAIEAADSDPSVQAVLIVGA 60

Query: 61  GRNFIAGADIREFGKPPVPPSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRIA 120
           GRNFIAGADIREFGKPPVPPSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYR+A
Sbjct: 61  GRNFIAGADIREFGKPPVPPSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRLA 120

Query: 121 VDGAKLGLPEVQLGLLPGAGGTQRTPRLIGAQAALDLILSGRHASAKEALAFGLIDRLGS 180
           VDGAKLGLPEVQLGLLPGAGGTQRTPRLIGAQAALDL+LSGRHA+A+EALA GL+DRLGS
Sbjct: 121 VDGAKLGLPEVQLGLLPGAGGTQRTPRLIGAQAALDLMLSGRHANAQEALALGLVDRLGS 180

Query: 181 SDDILAEGLAYVHELLAAHAPVRRTRDAAALSDRAASLAAVATARAETAKKSRGLFSPLK 240
           SDDILAEGLAYVHELLA HAPVRRTRDA AL+DRA+SLAAVATARAETAKKSRGLFSPLK
Sbjct: 181 SDDILAEGLAYVHELLAGHAPVRRTRDATALNDRASSLAAVATARAETAKKSRGLFSPLK 240

Query: 241 IVDAVEAAIEQPFDEGLRVERKLFLECIDSPQRAGLIHAFFAEREVLKAPETRAAKPRTL 300
           IVDAVEAAI QPF++GLR ER+LFLEC+DSPQRAGL+HAFFAEREVLKAPETR  KPR L
Sbjct: 241 IVDAVEAAIAQPFEDGLRRERQLFLECLDSPQRAGLVHAFFAEREVLKAPETRDTKPRAL 300

Query: 301 NTIGVVGGGTMGAGIAVAVLDAGLPVTMIERDDASLARGRAHIEKVYDGLIAKGRLSAEK 360
           N IGVVGGGTMGAGIAVAVLDAGLPVTMIERD+ASLARGRAHIEKVYDGLIAKGR+SAEK
Sbjct: 301 NAIGVVGGGTMGAGIAVAVLDAGLPVTMIERDEASLARGRAHIEKVYDGLIAKGRMSAEK 360

Query: 361 KAALMSRWSGSTSYDALAGADLVIEAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYLDI 420
           KA LM+RW+GSTSYDALA ADLVIEAVFEDL+VKQAVFAELDRVCK GAVLATNTSYLDI
Sbjct: 361 KAQLMARWTGSTSYDALADADLVIEAVFEDLSVKQAVFAELDRVCKPGAVLATNTSYLDI 420

Query: 421 DALASSVSRPADVIGLHFFSPANIMKLLEVVVPKQVSADVVATAFELAKKLRKTPVRAGV 480
           DA+A+S+SRPADVIGLHFFSPANIMKLLEVVVPK VSADVVATAFELAKKLRKTPVRAGV
Sbjct: 421 DAIAASISRPADVIGLHFFSPANIMKLLEVVVPKAVSADVVATAFELAKKLRKTPVRAGV 480

Query: 481 CDGFIGNRVLAVYRSAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARK 540
           CDGFIGNR+LAVYRSAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARK
Sbjct: 481 CDGFIGNRILAVYRSAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARK 540

Query: 541 RRAATRNPAARYVQIADRLCERGWFGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAERARA 600
           RRAATRNPAARYVQIADRLCERGWFGQK+GRGFYLYPEGSRSG PDPEVEAIIDAER RA
Sbjct: 541 RRAATRNPAARYVQIADRLCERGWFGQKTGRGFYLYPEGSRSGQPDPEVEAIIDAERVRA 600

Query: 601 GITPRSFTDEEIIRRYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYA 660
           GITPR F+D+EIIRRYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYA
Sbjct: 601 GITPREFSDDEIIRRYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYA 660

Query: 661 DMVGLPKILADIREFAKEDPLFWKPSPLLIELVERGADFASLNQS 705
           DM+GLP+ILADIREFAKEDPLFW+ SPLLI+LVERGADFASLN +
Sbjct: 661 DMIGLPRILADIREFAKEDPLFWRASPLLIDLVERGADFASLNHA 705


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: 1536
Number of extensions: 52
Number of successful extensions: 1
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: 706
Length adjustment: 39
Effective length of query: 667
Effective length of database: 667
Effective search space:   444889
Effective search space used:   444889
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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