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

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 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

GapMind for catabolism of small carbon sources