GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Burkholderia phytofirmans PsJN

Align 3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.157); 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); short-chain-enoyl-CoA hydratase (EC 4.2.1.150) (characterized)
to candidate BPHYT_RS09560 BPHYT_RS09560 3-hydroxyacyl-CoA dehydrogenase

Query= BRENDA::A4YDS4
         (651 letters)



>FitnessBrowser__BFirm:BPHYT_RS09560
          Length = 694

 Score =  176 bits (447), Expect = 2e-48
 Identities = 127/399 (31%), Positives = 200/399 (50%), Gaps = 26/399 (6%)

Query: 2   KVTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAMERIKWSLSKLRESGSLK-EGV 60
           +V VIG+G MG GIA     AG  V + +   E L + +  I+ +     + G LK E +
Sbjct: 295 QVAVIGAGTMGGGIAMNFINAGIPVTLLETKQEALDRGLATIRKNYEATVKKGKLKPEVL 354

Query: 61  EQVLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLPI 120
            Q +A I P T     LK +D ++EAV E+L +K   F+  +  A   A+LA+NTS+L +
Sbjct: 355 GQRMALITP-TLSYDDLKNADLIVEAVFEELGVKEQAFKRLDEVAKQGAILASNTSTLDV 413

Query: 121 SEIASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVKD 180
            +IA+  K PQ VVGMHFF+P  +M L+E+VRGK+T+ +V+ T   +AK + K  +V   
Sbjct: 414 DKIAAFTKRPQDVVGMHFFSPANVMKLLEVVRGKETAKDVLATVMNLAKKIKKTAVVSGV 473

Query: 181 VPGFFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLDIGYSV 240
             GF  NR++ + +    +++E+G    Q VD  AIE+ GF MG F ++D  G DIG+++
Sbjct: 474 CDGFIGNRMVEQYIRQALFMLEEGALPAQ-VD-KAIEKFGFAMGPFRMSDLAGNDIGWAI 531

Query: 241 WKAVTARGFKAFPCSSTEKLVSQGKLGVKSGSGYYQYPS------PGKFVRPTLPSTSK- 293
            K               ++L   G+ G K+G G+Y Y +      P K V   + + SK 
Sbjct: 532 RKRRYLEHPDMHYSKIADRLCETGRFGQKTGGGWYDYKAGDRTAYPSKVVDDMIVAFSKE 591

Query: 294 -----------KLGRYLISPAVNEVSYLLREGIVGK-DDAEKGCVLGLGLP---KGILSY 338
                      ++   L+   VNE + +L EGI  K  D +   + G G P    G + Y
Sbjct: 592 TDTERRKISDEEIVERLVFALVNEGAKILEEGIASKASDIDMVYLTGYGFPLYRGGPMLY 651

Query: 339 ADEIGIDVVVNTLEEMRQTSGMDHYSPDPLLLSMVKEGK 377
           AD +G+  V   +         D +   P +  +  + +
Sbjct: 652 ADTVGLYNVERAIRRYAARPNGDAWQLAPSIAELAAKNR 690



 Score =  104 bits (259), Expect = 2e-26
 Identities = 64/190 (33%), Positives = 104/190 (54%), Gaps = 6/190 (3%)

Query: 407 LAWIVLNRPTRYNAINGDMIREINQALDSLEEREDVRVIAITGQGRVFSAGADVTEFGSL 466
           +A I LN P   N +       I + ++  +    ++ I +TG G+ FS GAD+TEF   
Sbjct: 11  VAVITLNNPP-VNGLGLSTRAGIVEGVERAQNDPAIKAIVLTGAGKAFSGGADITEFN-- 67

Query: 467 TPVKAMIASRKFHEVFMKIQFLTKPVIAVINGLALGGGMELALSADFRVASKTAEMGQPE 526
           TP      +     V   ++   KPVIA I+ +A+GGG+ELAL A +R+A+  A++  PE
Sbjct: 68  TPKAGQEPT--LATVIKIVEGSAKPVIAAIHSVAMGGGLELALGAHYRIAAPGAQIALPE 125

Query: 527 INLGLIPGGGGTQRLSRLSG-RKGLELVLTGRRVKAEEAYRLGIVEFLAEPEELESEVRK 585
           + LG++PG GGTQRL R  G    L ++++G  V +E+    G+ + LA+ +  E+ +  
Sbjct: 126 VKLGILPGAGGTQRLPRAIGLEAALNMIVSGAPVMSEKLADSGLFDELAQGDLAEAALAF 185

Query: 586 LANAIAEKSP 595
                A++ P
Sbjct: 186 ARKVSAKEGP 195


Lambda     K      H
   0.316    0.134    0.377 

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: 956
Number of extensions: 57
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 651
Length of database: 694
Length adjustment: 39
Effective length of query: 612
Effective length of database: 655
Effective search space:   400860
Effective search space used:   400860
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

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:

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