Alignments for a candidate for ech in Pantoea rwandensis LMG 26275

GapMind for catabolism of small carbon sources

Alignments for a candidate for ech in Pantoea rwandensis LMG 26275

Align Fatty acid oxidation complex subunit alpha; EC 4.2.1.17; EC 5.1.2.3; EC 5.3.3.8; EC 1.1.1.35 (characterized)
to candidate WP_084938412.1 HA51_RS26560 fatty acid oxidation complex subunit alpha FadB

Query= SwissProt::P21177
         (729 letters)



>NCBI__GCF_002095475.1:WP_084938412.1
          Length = 727

 Score = 1084 bits (2804), Expect = 0.0
 Identities = 541/719 (75%), Positives = 619/719 (86%), Gaps = 1/719 (0%)

Query: 1   MLYKGDTLYLDWLEDGIAELVFDAPGSVNKLDTATVASLGEAIGVLEQQSDLKGLLLRSN 60
           MLY+GDTL + WL+DGIAELVFDAPGSVNKLDT TVASLGEA+G+LEQQ  L+GLLL S 
Sbjct: 1   MLYQGDTLSVHWLDDGIAELVFDAPGSVNKLDTKTVASLGEALGILEQQPALRGLLLSSA 60

Query: 61  KAAFIVGADITEFLSLFLVPEEQLSQWLHFANSVFNRLEDLPVPTIAAVNGYALGGGCEC 120
           K AFIVGADITEFLSLF  PEE+LSQWL FANS+FNRLEDLPVPT+AA++GYALGGGCEC
Sbjct: 61  KPAFIVGADITEFLSLFDAPEEKLSQWLAFANSIFNRLEDLPVPTVAAIDGYALGGGCEC 120

Query: 121 VLATDYRLATPDLRIGLPETKLGIMPGFGGSVRMPRMLGADSALEIIAAGKDVGADQALK 180
           VLATD+R+ATP  RIGLPETKLGIMPGFGGSVR+PR+LGADSALEIIAAGKD+  + ALK
Sbjct: 121 VLATDFRIATPTARIGLPETKLGIMPGFGGSVRLPRLLGADSALEIIAAGKDIDGNSALK 180

Query: 181 IGLVDGVVKAEKLVEGAKAVLRQAINGDLDWKAKRQPKLEPLKLSKIEATMSFTIAKGMV 240
           +GL+D VV ++KL   A  +L+ AI     W+ +R PKL PLKLS IEA MSFTIAK MV
Sbjct: 181 LGLIDAVVSSDKLRAAALTMLQDAI-AQGSWQVRRAPKLNPLKLSPIEAAMSFTIAKSMV 239

Query: 241 AQTAGKHYPAPITAVKTIEAAARFGREEALNLENKSFVPLAHTNEARALVGIFLNDQYVK 300
            QTAGKHYPAPITAVKTIEAAA   R++AL LE  +FVPLA ++ ARALVGIFLNDQYVK
Sbjct: 240 MQTAGKHYPAPITAVKTIEAAASLHRDDALKLETAAFVPLAQSDVARALVGIFLNDQYVK 299

Query: 301 GKAKKLTKDVETPKQAAVLGAGIMGGGIAYQSAWKGVPVVMKDINDKSLTLGMTEAAKLL 360
           G AKK +     P+QAAVLGAGIMGGGIAYQSAWKGVPV MKDIN ++LTLGMTEA+KLL
Sbjct: 300 GLAKKHSSAAGAPQQAAVLGAGIMGGGIAYQSAWKGVPVKMKDINPQALTLGMTEASKLL 359

Query: 361 NKQLERGKIDGLKLAGVISTIHPTLDYAGFDRVDIVVEAVVENPKVKKAVLAETEQKVRQ 420
           NKQLERGKIDG KLA V++TI PTLDYAGF+R D+VVEAVVENP++K  VLAETEQ +R+
Sbjct: 360 NKQLERGKIDGAKLASVLTTIQPTLDYAGFERTDVVVEAVVENPQIKAKVLAETEQHLRE 419

Query: 421 DTVLASNTSTIPISELANALERPENFCGMHFFNPVHRMPLVEIIRGEKSSDETIAKVVAW 480
           D +LASNTSTIPIS LA +L+RPENFCGMHFFNPV RMPLVE+IRGEK+S+ TI+KVVAW
Sbjct: 420 DAILASNTSTIPISLLAQSLQRPENFCGMHFFNPVPRMPLVEVIRGEKTSEATISKVVAW 479

Query: 481 ASKMGKTPIVVNDCPGFFVNRVLFPYFAGFSQLLRDGADFRKIDKVMEKQFGWPMGPAYL 540
           ASKMGKTPIVVNDCPGFFVNRVLFPYFA FS LLRDGADFR+IDKVMEKQFGWPMGPA+L
Sbjct: 480 ASKMGKTPIVVNDCPGFFVNRVLFPYFAAFSLLLRDGADFRQIDKVMEKQFGWPMGPAWL 539

Query: 541 LDVVGIDTAHHAQAVMAAGFPQRMQKDYRDAIDALFDANRFGQKNGLGFWRYKEDSKGKP 600
           LDVVGIDTAHHAQ VMA GFP RMQKDYRDAID LFDA RFGQKNG GF+ +++D KGK 
Sbjct: 540 LDVVGIDTAHHAQKVMAQGFPTRMQKDYRDAIDVLFDAQRFGQKNGKGFYLWEQDKKGKA 599

Query: 601 KKEEDAAVEDLLAEVSQPKRDFSEEEIIARMMIPMVNEVVRCLEEGIIATPAEADMALVY 660
           +K+ D AV+ LL  + +PKR FS+E+I  RMM+PM+NEVVRCLEE IIA+PAEADMALVY
Sbjct: 600 QKKADPAVDALLEPICEPKRVFSDEDIANRMMLPMLNEVVRCLEENIIASPAEADMALVY 659

Query: 661 GLGFPPFHGGAFRWLDTLGSAKYLDMAQQYQHLGPLYEVPEGLRNKARHNEPYYPPVEP 719
           GLGFPPF GGAFR++DTLG++  +D A++Y  LGPLY +PE L  KA  ++ +YP V+P
Sbjct: 660 GLGFPPFRGGAFRYMDTLGNSNVVDQAKRYIALGPLYTLPEQLVQKAHQHQSWYPAVQP 718


Lambda     K      H
   0.318    0.136    0.399 

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: 1492
Number of extensions: 49
Number of successful extensions: 2
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: 729
Length of database: 727
Length adjustment: 40
Effective length of query: 689
Effective length of database: 687
Effective search space:   473343
Effective search space used:   473343
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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