GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

Align 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate WP_068174326.1 HTA01S_RS19105 FAD-dependent oxidoreductase

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



>NCBI__GCF_001592305.1:WP_068174326.1
          Length = 684

 Score =  574 bits (1479), Expect = e-168
 Identities = 314/672 (46%), Positives = 420/672 (62%), Gaps = 12/672 (1%)

Query: 1   MTPNPSADVVSRELRGKVLLVTIDHAPVNALSADVRRGLLAAIEAADADKAVEAVLIVGA 60
           MTP      V  E  G + ++ ID+ P+NA SA VR+GL+AAIE    D  +E  +++GA
Sbjct: 1   MTPR-----VYLERDGGIAVIVIDNPPINAGSAAVRQGLMAAIETLRNDDTLEGAVLIGA 55

Query: 61  GRNFIAGADIREFGKPPVPPSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRIA 120
           G  FIAG+D+REFG+P   P LP V   IEAC KPVVAA+HGAA GGG E+AL    R+A
Sbjct: 56  GNTFIAGSDLREFGQPLTEPQLPAVIAAIEACGKPVVAALHGAAQGGGFELALGCDARVA 115

Query: 121 VDGAKLGLPEVQLGLLPGAGGTQRTPRLIGAQAALDLILSGRHASAKEALAFGLIDRLGS 180
             G  +GLPEV LG++PGAGGTQR PR++G   A+ +I SG    A  AL  GL+D + +
Sbjct: 116 APGTVVGLPEVTLGIIPGAGGTQRLPRIVGIPPAIRMICSGERVLAAAALEAGLVDLIAT 175

Query: 181 SDDILAEGLAYVHELLAAHAPVRRTRDAAALSDRAASLAAVATARAETAKKSRGLFSPLK 240
            + + +  +A+  +L       R  RD       +A +A   TA  +  K+   + +   
Sbjct: 176 GN-LRSAAVAHARQLKGQK---RLVRDRQVPPASSADVATATTAAPQAGKRRPAVQAA-- 229

Query: 241 IVDAVEAAIEQPFDEGLRVERKLFLECIDSPQRAGLIHAFFAEREVLKAPETRAAKPRTL 300
            +DA+ A  +  FD+GL  ER +F     S +   L H FFAERE  K P    A  R +
Sbjct: 230 -IDAITATAQVGFDDGLADERAVFQRLRVSREAFALRHQFFAERESAKHPSLGEATARPV 288

Query: 301 NTIGVVGGGTMGAGIAVAVLDAGLPVTMIERDDASLARGRAHIEKVYDGLIAKGRLSAEK 360
             + V+G GTMG+GIA+A LDAG  V ++E+D A+L RG   I   Y   +  G+LSA  
Sbjct: 289 ERVAVIGAGTMGSGIAIAALDAGYRVLLLEQDAAALERGTGRIHAHYASRVQGGKLSASA 348

Query: 361 KAALMSRWSGSTSYDALAGADLVIEAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYLDI 420
            AA  +R   S  +  LA ADLVIEAVFE+L VKQ VF  +D + + GAVLA+NTSYLD+
Sbjct: 349 AAACEARLQTSLDWADLASADLVIEAVFEELGVKQQVFQRIDALARPGAVLASNTSYLDL 408

Query: 421 DALASSVSRPADVIGLHFFSPANIMKLLEVVVPKQVSADVVATAFELAKKLRKTPVRAGV 480
           DA+A++ SRP DVIGLHFFSPA++MKL+EVV  +  + D +AT   + K+L+K PV  G 
Sbjct: 409 DAIAAATSRPHDVIGLHFFSPAHVMKLMEVVRGQSSAPDALATGLAVGKRLKKMPVLTGN 468

Query: 481 CDGFIGNRVLAVYRSAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARK 540
             GFIGNR+ A YR   + M+E+GA P Q+DAA+RAFGF MGPF V DL+G DI W  R+
Sbjct: 469 AFGFIGNRLYAAYRRQCECMVEEGAWPEQVDAALRAFGFAMGPFAVADLSGLDIAWRMRQ 528

Query: 541 RRAATRNPAARYVQIADRLCERGWFGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAERARA 600
            +AATR+P ARYV I DRLCE G  G+K+G G+Y YPEG +    D  V A+I   RA  
Sbjct: 529 AQAATRDPQARYVHIPDRLCEAGRLGRKTGAGYYRYPEGDQGPQVDEAVHALIAQARADK 588

Query: 601 GITPRSFTDEEIIRRYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYA 660
           G+ PR   D+EI+RR + A++NE A ++ E +A R  DVDV  + GYGFPR+ GGP+ +A
Sbjct: 589 GLQPRELGDDEIVRRALLAIVNEAALLLAEGVAERATDVDVVLVNGYGFPRWEGGPVFWA 648

Query: 661 DMVGLPKILADI 672
              G   +  D+
Sbjct: 649 RERGAAALQEDM 660


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: 1119
Number of extensions: 54
Number of successful extensions: 2
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: 684
Length adjustment: 39
Effective length of query: 667
Effective length of database: 645
Effective search space:   430215
Effective search space used:   430215
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 Apr 09 2024. 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