GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Caulobacter crescentus NA1000

Align 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate CCNA_03293 CCNA_03293 multifunctional fatty acid oxidation complex subunit alpha FadJ

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



>FitnessBrowser__Caulo:CCNA_03293
          Length = 696

 Score =  589 bits (1519), Expect = e-172
 Identities = 319/693 (46%), Positives = 438/693 (63%), Gaps = 12/693 (1%)

Query: 9   VVSRELRGKVLLVTIDHAPVNALSADVRRGLLAAIEAADADKAVEAVLIVGAGRNFIAGA 68
           V    + G + +VT++  PVNALSA VR GL  A +AA AD AV+A++++  G+ FIAGA
Sbjct: 11  VTDFSVEGDIGVVTLNSPPVNALSAAVREGLQGAFDAAIADAAVKAIVLICDGKTFIAGA 70

Query: 69  DIREFGKPPVPPSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRIAVDGAKLGL 128
           DI EFGK    PSL DV N IE   KPV+AAIHG ALGGGLEVAL A+YR+AV  AK GL
Sbjct: 71  DITEFGKAMTGPSLQDVQNVIENSPKPVIAAIHGTALGGGLEVALVANYRVAVPSAKAGL 130

Query: 129 PEVQLGLLPGAGGTQRTPRLIGAQAALDLILSGRHASAKEALAFGLIDRLGSSDDILAEG 188
           PEV +GLLPGAGGTQR PR++G + AL+++ +G+H  AK A A GL D L     +    
Sbjct: 131 PEVNIGLLPGAGGTQRLPRIVGVEKALEMVTTGQHVPAKAAHAMGLFDELVEEGKLREGA 190

Query: 189 LAYVHELLAAHAPVRRTRDAAALSDRAASLAAVATA-RAETAKKSRGLFSPLKIVDAVEA 247
           +A+   ++A + P+++ RD     + A     +  A R   AKK RG  +P   +  +EA
Sbjct: 191 IAFAKAVVAENRPLKKVRDLNEKVEAARGKPEIFEAFRKANAKKFRGFMAPENNIKCIEA 250

Query: 248 AIEQPFDEGLRVERKLFLECIDSPQRAGLIHAFFAEREVLKAPETRAAKPRT-LNTIGVV 306
           A+  PFDEGL+ ERKLF+E +   Q A   + FFAER+  K P+     P   +  +GV+
Sbjct: 251 AVNLPFDEGLKAERKLFMELMTGSQSAAQRYVFFAERQAAKIPDVPDDTPTIPVKKVGVI 310

Query: 307 GGGTMGAGIAVAVLDAGLPVTMIERDDASLARGRAHIEKVYDGLIAKGRLSAEKKAALMS 366
           G GTMG GIA+  L+AG+PVT+IE    +L RG   I K Y+    KGRL+ +     M+
Sbjct: 311 GAGTMGGGIAMNFLNAGIPVTIIEAKQENLERGVGIIRKNYENTAKKGRLTQDDVEKRMA 370

Query: 367 RWSGSTSYDALAGADLVIEAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYLDIDALASS 426
             + S   +ALA  D++IEAVFE + +K+ VF +LD++ K GA+LATNTSYLD+DA+A+ 
Sbjct: 371 LLTPSMEMEALADCDMIIEAVFELMEIKKEVFTKLDKIAKPGAILATNTSYLDVDAIAAV 430

Query: 427 VSRPADVIGLHFFSPANIMKLLEVVVPKQVSADVVATAFELAKKLRKTPVRAGVCDGFIG 486
            SRP  VIG HFFSPAN+M+LLE+V   + S DV+AT  +L+K + K PV  GVC GF+G
Sbjct: 431 TSRPESVIGTHFFSPANVMRLLELVRGDKTSKDVIATCMKLSKTIGKVPVLVGVCYGFVG 490

Query: 487 NRVLAVYRSAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARKRRAATR 546
           NR+LA  +  A  ++ +GA P+ +D  +  FG PMGPF + DLAG DIGW   K  ++T 
Sbjct: 491 NRMLAQRQREAQKLILEGAMPWDVDRVLYDFGLPMGPFAMSDLAGLDIGWDPAKTSSST- 549

Query: 547 NPAARYVQIADRLCERGWFGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAERARAGITPRS 606
                   + + LCE    GQK+G+GFY Y E +R+  P P VE +I     +  I  R 
Sbjct: 550 --------VREVLCEMDRRGQKNGKGFYDYDE-NRNAKPSPVVEEVIRDFAEKRQIQRRE 600

Query: 607 FTDEEIIRRYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYADMVGLP 666
            TD+EI+ R +  M+NEGA ++ E  A+R  D+D+ ++ GYG+P Y GGPM + ++VGL 
Sbjct: 601 ITDQEILERCLYPMVNEGAKILEEGKAIRASDIDIVWINGYGWPVYSGGPMFWGELVGLD 660

Query: 667 KILADIREFAKEDPLFWKPSPLLIELVERGADF 699
           K+LA +++F  E    +KPS LL  LV  G  F
Sbjct: 661 KVLAKMKQFHAELGDDFKPSALLERLVAEGKGF 693


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: 1053
Number of extensions: 52
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: 696
Length adjustment: 39
Effective length of query: 667
Effective length of database: 657
Effective search space:   438219
Effective search space used:   438219
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.

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