GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1922
          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 (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