GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB 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.

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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