GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fadB in Cupriavidus basilensis 4G11

Align 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate RR42_RS35270 RR42_RS35270 3-hydroxyacyl-CoA dehydrogenase

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



>lcl|FitnessBrowser__Cup4G11:RR42_RS35270 RR42_RS35270
           3-hydroxyacyl-CoA dehydrogenase
          Length = 693

 Score =  583 bits (1503), Expect = e-171
 Identities = 322/696 (46%), Positives = 434/696 (62%), Gaps = 12/696 (1%)

Query: 9   VVSRELRGKVLLVTIDHAPVNALSADVRRGLLAAIEAADADKAVEAVLIVGAGRNFIAGA 68
           V    + G++ ++T++  PVNALSA VR G+LA IE A AD  V  +++  AG+ FIAGA
Sbjct: 7   VADLAVEGEIAILTLNSPPVNALSAAVRAGILAGIERAIADSNVRGIVLTCAGKTFIAGA 66

Query: 69  DIREFGKPPVPPSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRIAVDGAKLGL 128
           DI EFGKPPV PSL DV   IE   KPVVAAIHG ALGGGLEVAL  HYR+A   A+ GL
Sbjct: 67  DITEFGKPPVGPSLADVQAAIEGSPKPVVAAIHGTALGGGLEVALVCHYRVAARSARCGL 126

Query: 129 PEVQLGLLPGAGGTQRTPRLIGAQAALDLILSGRHASAKEALAFGLIDRLGSSDDILAEG 188
           PEV LGLLPGAGGTQR PR++G   ALD++ SG H  A  A   GL D +     + A  
Sbjct: 127 PEVNLGLLPGAGGTQRLPRIVGPAKALDMVTSGAHIGAAAAAEMGLFDLVTEDAALRASA 186

Query: 189 LAYVHELLAAHAPVRRTRDAAALSDRAASLAAV-ATARAETAKKSRGLFSPLKIVDAVEA 247
           +A+  ++ A   P+R+ RD     + A     + A  R   A+K RG  +P   +  +EA
Sbjct: 187 IAFARQVNAEQRPLRKVRDLNEKVEAARGKPELFADFRRANARKFRGFDAPEYNIRCIEA 246

Query: 248 AIEQPFDEGLRVERKLFLECIDSPQRAGLIHAFFAEREVLKAPETRAAKPRT-LNTIGVV 306
           A+  PFDEG++VERKLFLE ++  Q A   + FFA R+V   P+  A  P   +  +G++
Sbjct: 247 AVNLPFDEGMKVERKLFLELMNGTQSAAQRYYFFASRQVWNVPDVPADTPVIDVKKVGII 306

Query: 307 GGGTMGAGIAVAVLDAGLPVTMIERDDASLARGRAHIEKVYDGLIAKGRLSAEKKAALMS 366
           G GTMG GIA+ +L+AG+PV ++E    +L RG   I   YD    KGR++A      M+
Sbjct: 307 GAGTMGGGIAMNMLNAGIPVVIVETAQQALDRGVRTIRANYDNTAKKGRITAADVDRRMA 366

Query: 367 RWSGSTSYDALAGADLVIEAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYLDIDALASS 426
             + +     LA ADLVIEAV+E++ VK+ +F +LD++ K GA+LATNTS LD++ +A +
Sbjct: 367 LLTPTLELGQLADADLVIEAVYENMDVKKDIFGKLDKIVKPGAILATNTSALDVNEIARA 426

Query: 427 VSRPADVIGLHFFSPANIMKLLEVVVPKQVSADVVATAFELAKKLRKTPVRAGVCDGFIG 486
            SRP  VIGLHFFSPAN+MKLLEVV   + +  V+ T+ ELA+K+ K     GVC GF+G
Sbjct: 427 TSRPESVIGLHFFSPANVMKLLEVVRGDKTAKPVIRTSMELARKIGKIAALVGVCPGFVG 486

Query: 487 NRVLAVYRSAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARKRRAATR 546
           NR+LA  +  A  ++ +GA P+ ID  +  FGFPMGPF + DLAG D+GW   K  +AT 
Sbjct: 487 NRMLAQRQREAQKLVLEGALPWDIDRVLYNFGFPMGPFAMSDLAGLDLGWIREKSSSAT- 545

Query: 547 NPAARYVQIADRLCERGWFGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAERARAGITPRS 606
                   + + LCE    GQK+G G+Y Y E  R+  P P VE II    AR G T R 
Sbjct: 546 --------LREILCEMDRRGQKTGAGYYDYDE-KRNAIPSPVVEGIIRDFAARQGKTSRV 596

Query: 607 FTDEEIIRRYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYADMVGLP 666
             ++EI+ R +  MINEGA ++ E  A+R  D+DV ++ GYG+P YRGGPM YAD +GL 
Sbjct: 597 VCEQEILERCIYPMINEGAKILEEGKAIRASDIDVVWVNGYGWPVYRGGPMCYADTIGLD 656

Query: 667 KILADIREFAKEDPLFWKPSPLLIELVERGADFASL 702
           K+LA ++ F       +KP+ LL +LV +G  F+ L
Sbjct: 657 KVLAVMKNFEATLGADFKPARLLEDLVAQGKKFSDL 692


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: 1100
Number of extensions: 68
Number of successful extensions: 6
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: 693
Length adjustment: 39
Effective length of query: 667
Effective length of database: 654
Effective search space:   436218
Effective search space used:   436218
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 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