Alignments for a candidate for paaH in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaH in Burkholderia phytofirmans PsJN

Align 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate BPHYT_RS09560 BPHYT_RS09560 3-hydroxyacyl-CoA dehydrogenase

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



>FitnessBrowser__BFirm:BPHYT_RS09560
          Length = 694

 Score =  592 bits (1526), Expect = e-173
 Identities = 317/687 (46%), Positives = 435/687 (63%), Gaps = 10/687 (1%)

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

Query: 78  V--PPSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRIAVDGAKLGLPEVQLGL 135
               P+L  V   +E   KPV+AAIH  A+GGGLE+AL AHYRIA  GA++ LPEV+LG+
Sbjct: 71  AGQEPTLATVIKIVEGSAKPVIAAIHSVAMGGGLELALGAHYRIAAPGAQIALPEVKLGI 130

Query: 136 LPGAGGTQRTPRLIGAQAALDLILSGRHASAKEALAFGLIDRLGSSDDILAEG-LAYVHE 194
           LPGAGGTQR PR IG +AAL++I+SG    +++    GL D L   D  LAE  LA+  +
Sbjct: 131 LPGAGGTQRLPRAIGLEAALNMIVSGAPVMSEKLADSGLFDELAQGD--LAEAALAFARK 188

Query: 195 LLAAHAPVRRTRDAAALSDRAASLAAVATARAETAKKSRGLFSPLKIVDAVEAAIEQPFD 254
           + A   P  + RD       AA    +  AR   A  ++   +PLK +DAVEA +++ FD
Sbjct: 189 VSAKEGPHPKVRDRKIEHPNAAGF--IQFARNTVATMAKNFPAPLKCIDAVEAGVQKGFD 246

Query: 255 EGLRVERKLFLECIDSPQRAGLIHAFFAEREVLKAPETRAAKP-RTLNTIGVVGGGTMGA 313
           +GL  ER+ F+  + +P+   L HAFF ER   K P+  +  P R +  + V+G GTMG 
Sbjct: 247 KGLAFERECFMALVQTPESHALRHAFFGERAASKIPDVPSDTPVRDIGQVAVIGAGTMGG 306

Query: 314 GIAVAVLDAGLPVTMIERDDASLARGRAHIEKVYDGLIAKGRLSAEKKAALMSRWSGSTS 373
           GIA+  ++AG+PVT++E    +L RG A I K Y+  + KG+L  E     M+  + + S
Sbjct: 307 GIAMNFINAGIPVTLLETKQEALDRGLATIRKNYEATVKKGKLKPEVLGQRMALITPTLS 366

Query: 374 YDALAGADLVIEAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYLDIDALASSVSRPADV 433
           YD L  ADL++EAVFE+L VK+  F  LD V K GA+LA+NTS LD+D +A+   RP DV
Sbjct: 367 YDDLKNADLIVEAVFEELGVKEQAFKRLDEVAKQGAILASNTSTLDVDKIAAFTKRPQDV 426

Query: 434 IGLHFFSPANIMKLLEVVVPKQVSADVVATAFELAKKLRKTPVRAGVCDGFIGNRVLAVY 493
           +G+HFFSPAN+MKLLEVV  K+ + DV+AT   LAKK++KT V +GVCDGFIGNR++  Y
Sbjct: 427 VGMHFFSPANVMKLLEVVRGKETAKDVLATVMNLAKKIKKTAVVSGVCDGFIGNRMVEQY 486

Query: 494 RSAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARKRRAATRNPAARYV 553
              A  M+E+GA P Q+D A+  FGF MGPF++ DLAG DIGWA RKRR    +P   Y 
Sbjct: 487 IRQALFMLEEGALPAQVDKAIEKFGFAMGPFRMSDLAGNDIGWAIRKRR-YLEHPDMHYS 545

Query: 554 QIADRLCERGWFGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAERARAGITPRSFTDEEII 613
           +IADRLCE G FGQK+G G+Y Y  G R+  P   V+ +I A         R  +DEEI+
Sbjct: 546 KIADRLCETGRFGQKTGGGWYDYKAGDRTAYPSKVVDDMIVAFSKETDTERRKISDEEIV 605

Query: 614 RRYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYADMVGLPKILADIR 673
            R + A++NEGA ++ E IA +  D+D+ +L GYGFP YRGGPM YAD VGL  +   IR
Sbjct: 606 ERLVFALVNEGAKILEEGIASKASDIDMVYLTGYGFPLYRGGPMLYADTVGLYNVERAIR 665

Query: 674 EF-AKEDPLFWKPSPLLIELVERGADF 699
            + A+ +   W+ +P + EL  +   F
Sbjct: 666 RYAARPNGDAWQLAPSIAELAAKNRGF 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: 1047
Number of extensions: 49
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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, 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

GapMind for catabolism of small carbon sources