GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Cup4G11:RR42_RS35270
          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:

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