GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Shewanella loihica PV-4

Align 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate 5210423 Shew_2864 3-hydroxyacyl-CoA dehydrogenase, NAD-binding (RefSeq)

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



>FitnessBrowser__PV4:5210423
          Length = 708

 Score =  545 bits (1403), Expect = e-159
 Identities = 302/700 (43%), Positives = 434/700 (62%), Gaps = 15/700 (2%)

Query: 13  ELRGKVLLVTIDHAPVNALSADVRRGLLAAIEAADADKAVEAVLIVGAGRNFIAGADIRE 72
           ++ G+  ++ ++  PVN+L   +R  LLA ++ A+AD++V+A+++  +G+ F  GADI E
Sbjct: 8   QIHGRTAVIILNQPPVNSLGLALRTHLLADLKRAEADESVDAIVLASSGKLFCGGADISE 67

Query: 73  FGKPPV--PPSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRIAVDGAKLGLPE 130
           F        P+LP VC+ +EA  K VVAA++G ALGGG E+ LA  YRIA+  AKLGLPE
Sbjct: 68  FSSDDALAEPNLPQVCDALEASPKLVVAAVNGLALGGGCELTLACDYRIALPAAKLGLPE 127

Query: 131 VQLGLLPGAGGTQRTPRLIGAQAALDLILSGRHASAKEALAFGLIDRL-GSSDDILAEGL 189
           V LG+LPGAGGTQR PR+ G Q AL++I SGR   A   L  G+ID L     + +   +
Sbjct: 128 VNLGILPGAGGTQRLPRIGGVQLALEMITSGRPLGAAAMLDAGVIDNLYQDGGNFIQAAV 187

Query: 190 AYVHELLAAHAPVRRTRDAAALSDRAASLAAVATARAETAKKSRGLFSPLKIVDAVEAAI 249
            +  EL+A H P R   + +  +   +S       RA  A++SRG ++P + + AVEAA 
Sbjct: 188 DFAQELVAQHKPKRSCFEMSVDTSNISS-EIFNEFRAAIARRSRGYYAPERCIQAVEAAC 246

Query: 250 EQPFDEGLRVERKLFLECIDSPQRAGLIHAFFAEREVLKAP--ETRAAKPRTLNTIGVVG 307
           E P  EGL+ E +LF+EC+D+PQ     H FFAER V K P    +    R +  + V+G
Sbjct: 247 ELPLAEGLKREHQLFMECLDTPQARAQQHLFFAERGVAKIPGINPKTTATREIRKVAVIG 306

Query: 308 GGTMGAGIAVAVLDAGLPVTMIERDDASLARGRAHIEKVYDGLIAKGRLSAEKKAALMSR 367
            GTMG GIA+  ++ G+P  +++ +  +L RG   I K Y+  + KG+LS  +    M+ 
Sbjct: 307 SGTMGGGIAMNFINVGIPTQILDLNGEALERGLGVIRKNYEYTLKKGKLSQAQLDERMAL 366

Query: 368 WSGSTSYDALAGADLVIEAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYLDIDALASSV 427
            SG+T Y  +A  DLVIEAVFE + +K+ VF  LD  CK GA+LATNTS LD+D +A+  
Sbjct: 367 LSGTTDYADIADVDLVIEAVFEKMEIKKQVFKTLDATCKPGAILATNTSTLDVDEIAAET 426

Query: 428 SRPADVIGLHFFSPANIMKLLEVVVPKQVSADVVATAFELAKKLRKTPVRAGVCDGFIGN 487
           SRP DV+GLHFFSPAN+M+LLE+V   + + D + T  +LA++++K PV +GVC GFIGN
Sbjct: 427 SRPQDVLGLHFFSPANVMRLLEIVRANKTAPDALLTTVQLAQRIKKVPVVSGVCWGFIGN 486

Query: 488 RVLAVYRSAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARK-RRAATR 546
           R    Y   + +++ +GASP QID     FG PMG   +VDLAG D+G   R+ R+A T 
Sbjct: 487 RATDSYLRESMSLILEGASPAQIDKVHTEFGMPMGLPSMVDLAGIDVGILTREDRKAFTT 546

Query: 547 NPAARYVQIADRLCERGWFGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAERARAGIT--- 603
           +    +  I  +L  +  +GQK+GRG Y+Y EG R    DPEV  +        G+T   
Sbjct: 547 DLDPSHFAILHKLYAKQRYGQKTGRGLYIY-EG-RDKQEDPEVLELAAEAAKEFGVTRRS 604

Query: 604 PRSFTDEEIIRRYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYADMV 663
           P   +D+EI+ R +  +INEGA ++ E IALR  D+D+   YG+GFP +RGGPM+YAD +
Sbjct: 605 PEQISDQEILERTIYPIINEGARILEEGIALRASDIDIVLAYGFGFPIFRGGPMQYADEI 664

Query: 664 GLPKILADI---REFAKEDPLFWKPSPLLIELVERGADFA 700
           GL ++L  +   R+   +  L++KP+PLL  LV+ G  FA
Sbjct: 665 GLERVLTALNKYRDTLDKGELWFKPAPLLERLVKEGKTFA 704


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: 1086
Number of extensions: 49
Number of successful extensions: 7
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: 708
Length adjustment: 39
Effective length of query: 667
Effective length of database: 669
Effective search space:   446223
Effective search space used:   446223
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: 55 (25.8 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