Alignments for a candidate for paaH in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaH in Caulobacter crescentus NA1000

Align 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate CCNA_03293 CCNA_03293 multifunctional fatty acid oxidation complex subunit alpha FadJ

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



>FitnessBrowser__Caulo:CCNA_03293
          Length = 696

 Score =  589 bits (1519), Expect = e-172
 Identities = 319/693 (46%), Positives = 438/693 (63%), Gaps = 12/693 (1%)

Query: 9   VVSRELRGKVLLVTIDHAPVNALSADVRRGLLAAIEAADADKAVEAVLIVGAGRNFIAGA 68
           V    + G + +VT++  PVNALSA VR GL  A +AA AD AV+A++++  G+ FIAGA
Sbjct: 11  VTDFSVEGDIGVVTLNSPPVNALSAAVREGLQGAFDAAIADAAVKAIVLICDGKTFIAGA 70

Query: 69  DIREFGKPPVPPSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRIAVDGAKLGL 128
           DI EFGK    PSL DV N IE   KPV+AAIHG ALGGGLEVAL A+YR+AV  AK GL
Sbjct: 71  DITEFGKAMTGPSLQDVQNVIENSPKPVIAAIHGTALGGGLEVALVANYRVAVPSAKAGL 130

Query: 129 PEVQLGLLPGAGGTQRTPRLIGAQAALDLILSGRHASAKEALAFGLIDRLGSSDDILAEG 188
           PEV +GLLPGAGGTQR PR++G + AL+++ +G+H  AK A A GL D L     +    
Sbjct: 131 PEVNIGLLPGAGGTQRLPRIVGVEKALEMVTTGQHVPAKAAHAMGLFDELVEEGKLREGA 190

Query: 189 LAYVHELLAAHAPVRRTRDAAALSDRAASLAAVATA-RAETAKKSRGLFSPLKIVDAVEA 247
           +A+   ++A + P+++ RD     + A     +  A R   AKK RG  +P   +  +EA
Sbjct: 191 IAFAKAVVAENRPLKKVRDLNEKVEAARGKPEIFEAFRKANAKKFRGFMAPENNIKCIEA 250

Query: 248 AIEQPFDEGLRVERKLFLECIDSPQRAGLIHAFFAEREVLKAPETRAAKPRT-LNTIGVV 306
           A+  PFDEGL+ ERKLF+E +   Q A   + FFAER+  K P+     P   +  +GV+
Sbjct: 251 AVNLPFDEGLKAERKLFMELMTGSQSAAQRYVFFAERQAAKIPDVPDDTPTIPVKKVGVI 310

Query: 307 GGGTMGAGIAVAVLDAGLPVTMIERDDASLARGRAHIEKVYDGLIAKGRLSAEKKAALMS 366
           G GTMG GIA+  L+AG+PVT+IE    +L RG   I K Y+    KGRL+ +     M+
Sbjct: 311 GAGTMGGGIAMNFLNAGIPVTIIEAKQENLERGVGIIRKNYENTAKKGRLTQDDVEKRMA 370

Query: 367 RWSGSTSYDALAGADLVIEAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYLDIDALASS 426
             + S   +ALA  D++IEAVFE + +K+ VF +LD++ K GA+LATNTSYLD+DA+A+ 
Sbjct: 371 LLTPSMEMEALADCDMIIEAVFELMEIKKEVFTKLDKIAKPGAILATNTSYLDVDAIAAV 430

Query: 427 VSRPADVIGLHFFSPANIMKLLEVVVPKQVSADVVATAFELAKKLRKTPVRAGVCDGFIG 486
            SRP  VIG HFFSPAN+M+LLE+V   + S DV+AT  +L+K + K PV  GVC GF+G
Sbjct: 431 TSRPESVIGTHFFSPANVMRLLELVRGDKTSKDVIATCMKLSKTIGKVPVLVGVCYGFVG 490

Query: 487 NRVLAVYRSAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARKRRAATR 546
           NR+LA  +  A  ++ +GA P+ +D  +  FG PMGPF + DLAG DIGW   K  ++T 
Sbjct: 491 NRMLAQRQREAQKLILEGAMPWDVDRVLYDFGLPMGPFAMSDLAGLDIGWDPAKTSSST- 549

Query: 547 NPAARYVQIADRLCERGWFGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAERARAGITPRS 606
                   + + LCE    GQK+G+GFY Y E +R+  P P VE +I     +  I  R 
Sbjct: 550 --------VREVLCEMDRRGQKNGKGFYDYDE-NRNAKPSPVVEEVIRDFAEKRQIQRRE 600

Query: 607 FTDEEIIRRYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYADMVGLP 666
            TD+EI+ R +  M+NEGA ++ E  A+R  D+D+ ++ GYG+P Y GGPM + ++VGL 
Sbjct: 601 ITDQEILERCLYPMVNEGAKILEEGKAIRASDIDIVWINGYGWPVYSGGPMFWGELVGLD 660

Query: 667 KILADIREFAKEDPLFWKPSPLLIELVERGADF 699
           K+LA +++F  E    +KPS LL  LV  G  F
Sbjct: 661 KVLAKMKQFHAELGDDFKPSALLERLVAEGKGF 693


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: 1053
Number of extensions: 52
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:

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