GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaH 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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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