Alignments for a candidate for paaH in Paraburkholderia phymatum STM815

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaH in Paraburkholderia phymatum STM815

Align 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate WP_012406378.1 BPHY_RS35840 3-hydroxyacyl-CoA dehydrogenase

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



>NCBI__GCF_000020045.1:WP_012406378.1
          Length = 706

 Score = 1092 bits (2825), Expect = 0.0
 Identities = 541/706 (76%), Positives = 621/706 (87%)

Query: 1   MTPNPSADVVSRELRGKVLLVTIDHAPVNALSADVRRGLLAAIEAADADKAVEAVLIVGA 60
           MT  P A  V+ ELRG +LLVT+D+ PVNAL  +VRRGL+AAIEAA+A    +AVLIVGA
Sbjct: 1   MTSTPDAAPVNCELRGNLLLVTVDNPPVNALGVEVRRGLVAAIEAAEAYAVAKAVLIVGA 60

Query: 61  GRNFIAGADIREFGKPPVPPSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRIA 120
           GRNFIAGADIREFGKPP  P+LPDVCNRIEAC+KPV+ AIHGAALGGGLE+ALAAHYR+A
Sbjct: 61  GRNFIAGADIREFGKPPQMPTLPDVCNRIEACSKPVIVAIHGAALGGGLEIALAAHYRLA 120

Query: 121 VDGAKLGLPEVQLGLLPGAGGTQRTPRLIGAQAALDLILSGRHASAKEALAFGLIDRLGS 180
           V GAKLGLPEV LGLLPGAGGTQR PRLIGA+AAL L+LSG+H  A++AL  GL+DR+G 
Sbjct: 121 VAGAKLGLPEVLLGLLPGAGGTQRAPRLIGAEAALSLMLSGKHIGAQDALKMGLVDRVGQ 180

Query: 181 SDDILAEGLAYVHELLAAHAPVRRTRDAAALSDRAASLAAVATARAETAKKSRGLFSPLK 240
           SDD+L EGL Y  +LL+ HAPVRRTRDA  L+D  A  AA+A ARA+TAKKSRGL SPLK
Sbjct: 181 SDDVLTEGLTYAQQLLSEHAPVRRTRDAQGLADTDAGAAAIAVARADTAKKSRGLLSPLK 240

Query: 241 IVDAVEAAIEQPFDEGLRVERKLFLECIDSPQRAGLIHAFFAEREVLKAPETRAAKPRTL 300
           IVD V AA+  PF++GLR ER  F+EC+DSPQRA L+HAF AER+V KAPETR+A+PR +
Sbjct: 241 IVDCVNAALTLPFEDGLRFERARFIECLDSPQRAALVHAFQAERQVQKAPETRSAQPRPI 300

Query: 301 NTIGVVGGGTMGAGIAVAVLDAGLPVTMIERDDASLARGRAHIEKVYDGLIAKGRLSAEK 360
            + GVVGGGTMGAGIAVA+LDAGLPVTMIERDDASLARGRAH++KVYDGLIAKGRL+ + 
Sbjct: 301 ASAGVVGGGTMGAGIAVALLDAGLPVTMIERDDASLARGRAHVDKVYDGLIAKGRLTHDA 360

Query: 361 KAALMSRWSGSTSYDALAGADLVIEAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYLDI 420
           KA  ++R++GSTSYDALA AD+VIEAVFED+AVKQAVFAELDRVCK GAVLATNTSYLDI
Sbjct: 361 KAKKLARFAGSTSYDALAEADVVIEAVFEDMAVKQAVFAELDRVCKPGAVLATNTSYLDI 420

Query: 421 DALASSVSRPADVIGLHFFSPANIMKLLEVVVPKQVSADVVATAFELAKKLRKTPVRAGV 480
           DA+A+ ++RP DVIGLHFFSPA++MKLLEVVVP +VSADVVATAF+LAKKLRK PVRAGV
Sbjct: 421 DAIAAGIARPQDVIGLHFFSPAHVMKLLEVVVPARVSADVVATAFDLAKKLRKVPVRAGV 480

Query: 481 CDGFIGNRVLAVYRSAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARK 540
           CDGFIGNR+LAVYR+AAD +ME+GASPYQID AVR  GFPMGP+QV+DLAGGDIGWA RK
Sbjct: 481 CDGFIGNRMLAVYRAAADHLMEEGASPYQIDKAVRELGFPMGPYQVIDLAGGDIGWATRK 540

Query: 541 RRAATRNPAARYVQIADRLCERGWFGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAERARA 600
           RRA+TR+P ARYVQI DRLCERGWFGQK+ RGFY Y  G R+GTPDPEVEAIIDAER RA
Sbjct: 541 RRASTRDPNARYVQIPDRLCERGWFGQKTSRGFYRYEAGQRAGTPDPEVEAIIDAERERA 600

Query: 601 GITPRSFTDEEIIRRYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYA 660
           GITPR+F+DE+I+RRYMAAMINEGANV+HERIALRPLDVDVT + G+GFP +RGGPM YA
Sbjct: 601 GITPRAFSDEQIVRRYMAAMINEGANVIHERIALRPLDVDVTLMNGFGFPAWRGGPMHYA 660

Query: 661 DMVGLPKILADIREFAKEDPLFWKPSPLLIELVERGADFASLNQSV 706
           D +GLP +LADIREF K DPLFWKPSPLL+ELVERG  FASLN+++
Sbjct: 661 DTIGLPALLADIREFEKRDPLFWKPSPLLVELVERGETFASLNRAM 706


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: 1374
Number of extensions: 46
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 24 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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 catabolism of small carbon sources