Alignments for a candidate for fadA in Pantoea rwandensis LMG 26275

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Pantoea rwandensis LMG 26275

Align long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211); acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate WP_084938412.1 HA51_RS26560 fatty acid oxidation complex subunit alpha FadB

Query= BRENDA::Q64428
         (763 letters)



>NCBI__GCF_002095475.1:WP_084938412.1
          Length = 727

 Score =  375 bits (964), Expect = e-108
 Identities = 251/725 (34%), Positives = 391/725 (53%), Gaps = 45/725 (6%)

Query: 49  VAVIRINSPNSKVNTLNKEVQSEFVEVMNEIWANDQIRSAVLISSKPGCFVAGADIN-ML 107
           +A +  ++P S VN L+ +  +   E +  +     +R  +L S+KP  F+ GADI   L
Sbjct: 17  IAELVFDAPGS-VNKLDTKTVASLGEALGILEQQPALRGLLLSSAKPA-FIVGADITEFL 74

Query: 108 ASCTTPQEAARISQE---GQKMFEKLEKSPKPVVAAISGSCLGGGLELAIACQYRIATKD 164
           +    P+E  ++SQ       +F +LE  P P VAAI G  LGGG E  +A  +RIAT  
Sbjct: 75  SLFDAPEE--KLSQWLAFANSIFNRLEDLPVPTVAAIDGYALGGGCECVLATDFRIATPT 132

Query: 165 RKTVLGVPEVLLGILPGAGGTQRLPKMVGVPAAFDMMLTGRNIRADRAKKMGLVDQLVDP 224
            +  +G+PE  LGI+PG GG+ RLP+++G  +A +++  G++I  + A K+GL+D +V  
Sbjct: 133 AR--IGLPETKLGIMPGFGGSVRLPRLLGADSALEIIAAGKDIDGNSALKLGLIDAVV-- 188

Query: 225 LGPGIKSPEERTIEYLEEVAVNFAKGLADRKVSAKQSKGLMEKLTSYAMTIPFVRQQVYK 284
                 S ++     L  +    A+G    + + K +   +  + + AM+    +  V +
Sbjct: 189 ------SSDKLRAAALTMLQDAIAQGSWQVRRAPKLNPLKLSPIEA-AMSFTIAKSMVMQ 241

Query: 285 TVEEKVKKQTKGLYPAPLKIIDAVKTGLEQGNDAGYLAESEKFGELALTKESKALMGLY- 343
           T  +         YPAP+  +  ++       D     E+  F  LA +  ++AL+G++ 
Sbjct: 242 TAGKH--------YPAPITAVKTIEAAASLHRDDALKLETAAFVPLAQSDVARALVGIFL 293

Query: 344 NGQV---LCKKNK--FGAPQKTVQQLAILGAGLMGAGIAQVSVDKGLKTLLKDTTVTGLG 398
           N Q    L KK+    GAP    QQ A+LGAG+MG GIA  S  KG+   +KD     L 
Sbjct: 294 NDQYVKGLAKKHSSAAGAP----QQAAVLGAGIMGGGIAYQSAWKGVPVKMKDINPQALT 349

Query: 399 RGQQQVFKGLNDKVKKKALTSFERDSIFSNLIGQLDYKGFEKADMVIEAVFEDLAVKHKV 458
            G  +  K LN ++++  +   +  S+ + +   LDY GFE+ D+V+EAV E+  +K KV
Sbjct: 350 LGMTEASKLLNKQLERGKIDGAKLASVLTTIQPTLDYAGFERTDVVVEAVVENPQIKAKV 409

Query: 459 LKEVESVTPEHCIFASNTSALPINQIAAVSQRPEKVIGMHYFSPVDKMQLLEIITTDKTS 518
           L E E    E  I ASNTS +PI+ +A   QRPE   GMH+F+PV +M L+E+I  +KTS
Sbjct: 410 LAETEQHLREDAILASNTSTIPISLLAQSLQRPENFCGMHFFNPVPRMPLVEVIRGEKTS 469

Query: 519 KDTTASAVAVGLKQGKVIIVVKDGPGFYTTRCLAPMMSEVIRILQEGVDPKKLD-ALTTG 577
           + T +  VA   K GK  IVV D PGF+  R L P  +    +L++G D +++D  +   
Sbjct: 470 EATISKVVAWASKMGKTPIVVNDCPGFFVNRVLFPYFAAFSLLLRDGADFRQIDKVMEKQ 529

Query: 578 FGFPVGAATLADEVGIDVAQHVAEDLGKAFGERFGGGSVELLKLMVSKGFLGRKSGKGFY 637
           FG+P+G A L D VGID A H  + + + F  R      + + ++      G+K+GKGFY
Sbjct: 530 FGWPMGPAWLLDVVGIDTAHHAQKVMAQGFPTRMQKDYRDAIDVLFDAQRFGQKNGKGFY 589

Query: 638 IYQ---SGSKNKNLNSEIDNILVNLRLPAKPEVSSDEDIQYRVITRFVNEAVLCLQEGIL 694
           +++    G   K  +  +D +L  +  P +  V SDEDI  R++   +NE V CL+E I+
Sbjct: 590 LWEQDKKGKAQKKADPAVDALLEPICEPKR--VFSDEDIANRMMLPMLNEVVRCLEENII 647

Query: 695 ATPEEGDIGAVFGLGFPPCLGGPFRFVDLYGAQKVVDRLRKYESAYGTQFT-PCQLLRDL 753
           A+P E D+  V+GLGFPP  GG FR++D  G   VVD+ ++Y  A G  +T P QL++  
Sbjct: 648 ASPAEADMALVYGLGFPPFRGGAFRYMDTLGNSNVVDQAKRY-IALGPLYTLPEQLVQKA 706

Query: 754 ANNSS 758
             + S
Sbjct: 707 HQHQS 711


Lambda     K      H
   0.317    0.135    0.380 

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: 1056
Number of extensions: 50
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 763
Length of database: 727
Length adjustment: 40
Effective length of query: 723
Effective length of database: 687
Effective search space:   496701
Effective search space used:   496701
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 bits)

This GapMind analysis is from Sep 24 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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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