GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fadB in Pseudomonas fluorescens FW300-N2E2

Align 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate Pf6N2E2_1922 Enoyl-CoA hydratase (EC 4.2.1.17) / Delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase (EC 5.3.3.8) / 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) / 3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3)

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



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1922 Enoyl-CoA hydratase
           (EC 4.2.1.17) / Delta(3)-cis-delta(2)-trans-enoyl-CoA
           isomerase (EC 5.3.3.8) / 3-hydroxyacyl-CoA dehydrogenase
           (EC 1.1.1.35) / 3-hydroxybutyryl-CoA epimerase (EC
           5.1.2.3)
          Length = 703

 Score =  540 bits (1390), Expect = e-157
 Identities = 301/701 (42%), Positives = 422/701 (60%), Gaps = 6/701 (0%)

Query: 9   VVSRELRGKVLLVTIDHAPVNALSADVRRGLLAAIEAADADKAVEAVLIVGAGRNFIAGA 68
           +VS E+ G V ++T+++ PVNAL+ ++R  ++ A+  A+AD AV A++++G G+NFIAGA
Sbjct: 6   MVSYEVEGVVAVITVNNPPVNALTPEMRGSIIDAVTHANADPAVAAIVLMGGGQNFIAGA 65

Query: 69  DIREFGKPPVPPSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRIAVDGAKLGL 128
           DIR+FGK     +       ++A  KP VAAIHG ALGGGLE ALA HYRIA+  AKLGL
Sbjct: 66  DIRQFGKARTITTSMSAA-ALDASAKPTVAAIHGYALGGGLEHALACHYRIALPTAKLGL 124

Query: 129 PEVQLGLLPGAGGTQRTPRLIGAQAALDLILSGRHASAKEALAFGLIDRL--GSSDDILA 186
           PEV LGL+PG GGTQR PRL+GA  A DL++S RH  A EAL  GLI ++  G+ +  L 
Sbjct: 125 PEVALGLIPGGGGTQRLPRLVGAAVATDLLVSSRHIHAPEALQIGLISQIVPGTQNQELR 184

Query: 187 EGLAYVHELLAAHAPVRRTRDAAALSDRAASLAAVATARAETAKKSRGLFSPLKIVDAVE 246
           +  A  +    AHA  +R RD A     A ++  +  AR E AKKS    +P   +D +E
Sbjct: 185 DA-AVRYAKAVAHAQPQRVRDLALEPMDATTMDLLQAARREAAKKSPHNKAPQYAIDCIE 243

Query: 247 AAIEQPFDEGLRVERKLFLECIDSPQRAGLIHAFFAEREVLKAPETRAA-KPRTLNTIGV 305
           AA   PFDE L VE +LF E   S     L +AFFAERE  K P+     KP  + +  V
Sbjct: 244 AAFNLPFDEALEVESRLFSELEGSDVAKALRYAFFAEREAAKVPDAPPGFKPAGVTSAAV 303

Query: 306 VGGGTMGAGIAVAVLDAGLPVTMIERDDASLARGRAHIEKVYDGLIAKGRLSAEKKAALM 365
           +G GTMGAGIA+   DAG+ V ++E    +L RG   I  +Y   + +GR++ ++  A +
Sbjct: 304 IGAGTMGAGIAICFADAGIVVKLLEASAEALDRGLQRIRDIYAVKVKRGRMTVQEMDACL 363

Query: 366 SRWSGSTSYDALAGADLVIEAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYLDIDALAS 425
                 + Y+ +   D+V+EAVFE + +K+ VF +LD V K GA+L TN+S +DI+ +A+
Sbjct: 364 QFVQPVSHYEEIGDCDVVVEAVFERIDLKKDVFTKLDAVMKPGALLLTNSSAIDINVMAN 423

Query: 426 SVSRPADVIGLHFFSPANIMKLLEVVVPKQVSADVVATAFELAKKLRKTPVRAGVCDGFI 485
              RP  V G HFF+PAN MKL E+V   Q S + V  A ++ + L+K    +G CDGF 
Sbjct: 424 MTGRPQSVAGAHFFAPANAMKLCEIVKGDQTSIETVVRAMKMGRDLKKVCAVSGTCDGFA 483

Query: 486 GNRVLAVYRSAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARKRRAAT 545
            NR  A   +    ++E+GA P QID  +  FG+PMGPF V DL+G D+ +  RKRRAA 
Sbjct: 484 ANRSRAPLVTEMMLLLEEGARPEQIDRVMVEFGYPMGPFAVSDLSGLDVSYDTRKRRAAA 543

Query: 546 RNPAARYVQIADRLCERGWFGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAERARAGITPR 605
            +P  R + + DR+ E G  GQK+G G+Y Y EG R+   D EV  II       G   R
Sbjct: 544 -DPQYRKLHVPDRMVELGRKGQKNGAGWYRYEEGDRTPRHDEEVMRIIATVAHELGTPQR 602

Query: 606 SFTDEEIIRRYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYADMVGL 665
           +FTD EI++R + A INE   ++ E  A R  D+DV +LYG+GFPR+RGG + +AD +G 
Sbjct: 603 TFTDSEILKRLLFASINEACKILDEGKAYRASDIDVMWLYGFGFPRHRGGLLYWADTIGA 662

Query: 666 PKILADIREFAKEDPLFWKPSPLLIELVERGADFASLNQSV 706
            +I   ++++ ++    W PSPLL +    G     L   +
Sbjct: 663 TEIHLQVQQWHEQYGRRWAPSPLLSKAANEGLSLRELKSVI 703


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: 1109
Number of extensions: 56
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: 703
Length adjustment: 39
Effective length of query: 667
Effective length of database: 664
Effective search space:   442888
Effective search space used:   442888
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, the preprint 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