Aligments for a candidate for fadB in Cupriavidus basilensis 4G11

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_RS22630 RR42_RS22630 3-hydroxyacyl-CoA dehydrogenase

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



>FitnessBrowser__Cup4G11:RR42_RS22630
          Length = 696

 Score =  603 bits (1554), Expect = e-176
 Identities = 337/692 (48%), Positives = 443/692 (64%), Gaps = 17/692 (2%)

Query: 15  RGKVLLVTIDHAPVNALSADVRRGLLAAIEAADADKAVEAVLIVGAGRNFIAGADIREFG 74
           +G++ ++ +D+ PVN L   VR GL   I  A  D AV A++I+GAG+ F  GADIR+F 
Sbjct: 9   QGRIAILLLDNPPVNGLGDTVRLGLFDGIAQATQDDAVAAIVILGAGKVFCGGADIRQFN 68

Query: 75  KPPVP--PSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRIAVDGAKLGLPEVQ 132
            P     P+L  V  RIE   KPVVAAIHG ALGGG+E+AL  HYRIA   A LGLPEV 
Sbjct: 69  APAASAQPTLRQVIARIEQSAKPVVAAIHGVALGGGMELALGCHYRIASADASLGLPEVN 128

Query: 133 LGLLPGAGGTQRTPRLIGAQAALDLILSGRHASAKEALAFGLIDRLGSSDDILAEGLAYV 192
           LGL+PG GGTQR PRLIG  AAL+LI  G+     +A+A G+ D L   D  LA  +A+ 
Sbjct: 129 LGLVPGGGGTQRLPRLIGVPAALELIQGGKPVRGDKAVALGMADALIDGDP-LAAAMAFA 187

Query: 193 HE---LLAAHAPVRRT--RDAAALSDRAASLAAVATARAETAKKSRGLFSPLKIVDAVEA 247
                L  AH  + R    DAA +   A S A  A AR   A+++         +  V+A
Sbjct: 188 ERVAGLPGAHPVIARRPCADAAGVDFAARSAAVSAKARNALAQRAA--------IACVQA 239

Query: 248 AIEQPFDEGLRVERKLFLECIDSPQRAGLIHAFFAEREVLKAPETRA-AKPRTLNTIGVV 306
           A   P D GL  ER  F + + S +   L H FFAERE  K     A A  RT+  +G++
Sbjct: 240 ATRLPIDAGLDDERARFDQLVASTESKALRHLFFAEREAPKVAALPAGASLRTVARVGIL 299

Query: 307 GGGTMGAGIAVAVLDAGLPVTMIERDDASLARGRAHIEKVYDGLIAKGRLSAEKKAALMS 366
           G GTMGAGIA+A  +AG+ VT++E+  A+L RG A I + Y+   AKG+L+A++ A  M+
Sbjct: 300 GAGTMGAGIAMAFANAGIAVTLLEQQQAALDRGLAMIRRNYEITAAKGKLTAQEIAQRMA 359

Query: 367 RWSGSTSYDALAGADLVIEAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYLDIDALASS 426
             + + +  ALA ADLVIEAVFED+AVK+AVFA LD +CK GA+LATNTS L ID +A+S
Sbjct: 360 CITPTLADAALADADLVIEAVFEDMAVKKAVFARLDALCKPGAILATNTSRLSIDVIAAS 419

Query: 427 VSRPADVIGLHFFSPANIMKLLEVVVPKQVSADVVATAFELAKKLRKTPVRAGVCDGFIG 486
            SRP DVIGLHFFSPAN+MKLLEVV  ++ + +V+AT  ++A+ + K PV   VC+GF+G
Sbjct: 420 TSRPQDVIGLHFFSPANVMKLLEVVQGERTAPEVIATCMKMARAIGKIPVLVRVCEGFVG 479

Query: 487 NRVLAVYRSAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARKRRAATR 546
           NR+L  Y   A  ++E+GASP Q+D A+  FG  MGP  + DLAG DI WA RKR A TR
Sbjct: 480 NRMLTPYWREAGFLLEEGASPQQVDGALTRFGMAMGPLAMADLAGMDINWATRKRLAPTR 539

Query: 547 NPAARYVQIADRLCERGWFGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAERARAGITPRS 606
               RY ++ADR+CE+G FGQK+  G+Y Y  GSR+  PDP V+A+I A  A AGI  R 
Sbjct: 540 PAHLRYSKVADRICEQGRFGQKTNAGYYRYEAGSRAPLPDPAVDALIRACAAEAGIERRE 599

Query: 607 FTDEEIIRRYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYADMVGLP 666
            +DEEI+ R M A+ NEGA ++ E IA R  D+DV +++GYGFP +RGGPM +A+ +GL 
Sbjct: 600 VSDEEIVERCMLALANEGARILEEGIARRAADIDVVYVHGYGFPAWRGGPMFHAETIGLG 659

Query: 667 KILADIREFAKEDPLFWKPSPLLIELVERGAD 698
           + L  IR         W P+PLL+ LV +G +
Sbjct: 660 RTLEKIRALNAIHGEHWTPAPLLVRLVAQGRE 691


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: 1143
Number of extensions: 53
Number of successful extensions: 5
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: 696
Length adjustment: 39
Effective length of query: 667
Effective length of database: 657
Effective search space:   438219
Effective search space used:   438219
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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