Alignments for a candidate for paaH in Rhizobium leguminosarum bv. trifolii WSM1325

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaH in Rhizobium leguminosarum bv. trifolii WSM1325

Align fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized)
to candidate WP_012755969.1 RLEG_RS01235 3-hydroxyacyl-CoA dehydrogenase NAD-binding domain-containing protein

Query= CharProtDB::CH_003230
         (714 letters)



>NCBI__GCF_000023185.1:WP_012755969.1
          Length = 737

 Score =  405 bits (1040), Expect = e-117
 Identities = 258/726 (35%), Positives = 384/726 (52%), Gaps = 33/726 (4%)

Query: 7   FTLNVRLDNIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKELRGVVFVSAKPDNFI 66
           FTL    D IA++T D+PG+ MN   AE  +++ AII     +  ++GVVF S K  +F 
Sbjct: 6   FTLETDADGIALVTWDMPGKSMNVFTAEVMAELDAIIDATTADAAVKGVVFTSGK-SSFS 64

Query: 67  AGADINMIGNCKTAQEAE-------------ALARQGQQLMAEIHALPIQVIAAIHGACL 113
            GAD++MI +  ++ + E              L  +   L  ++       ++AI+G C+
Sbjct: 65  GGADLSMIKSMFSSYQEEKAKSPETAVQNLFGLVGRMSGLFRKLEISGKPWVSAINGTCM 124

Query: 114 GGGLELALACHGRVCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGKQ 173
           GG  EL+LACHGRV ++     + LPEV++G+ PG+GGTQR+PRL     AL+M+ TG+ 
Sbjct: 125 GGAFELSLACHGRVASNAKSVKIALPEVKVGIFPGAGGTQRVPRLANAQDALQMMTTGQS 184

Query: 174 LRAKQALKLGLVDDVVPHSILLEAAVELAKKERPSSRPL-PVRERILAGPLG------RA 226
           L   +A  + LV  VV    L+ AA ++ K      +P+ P  E+    P G       A
Sbjct: 185 LTGSRAKAMNLVHQVVEPDQLIPAAKQMIKD---GLKPVAPWDEKGFKAPGGGIWTPASA 241

Query: 227 LLFKMVGKKTEHKTQGNYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQS-QAL 285
            L+         +T GNYPA   IL+ V  GL     +G   E R F E+  T ++   +
Sbjct: 242 QLWPAAPAILRRETSGNYPAALAILKCVYEGLQVPFDTGLKIEQRYFTEVLQTREAFSMI 301

Query: 286 RSIFFASTDVKKDPGSDAPPAP--LNSVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQ 343
           RS+F +  ++ K     A  A   L  VG++G G MG  IAYVTA  AGIPV + D + +
Sbjct: 302 RSLFISMQELGKGARRPAGHAKTELKHVGVVGAGFMGASIAYVTAA-AGIPVTLIDRDIE 360

Query: 344 GINHALKYSWDQLEGKVRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENLELK 403
                   S   ++  + +  L   E    L+ I+ + DY   A+ DL+IEAVFE+ E+K
Sbjct: 361 AATKGKTVSEGLVKDSIGKGRLTQDEAAALLSRITPSADYADLANADLVIEAVFEDREVK 420

Query: 404 QQMVAEVEQNCAAHTIFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHA 463
           + ++  VE       IFASNTS+LPI  +A ++ RP   IG+HFFSPVEKM L E+I  +
Sbjct: 421 KAVIEAVEAVLPEGAIFASNTSTLPISGLAKNSKRPADFIGIHFFSPVEKMMLTEVILGS 480

Query: 464 GTSAQTIATTVKLAKKQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHIDAAL 523
            T  + +A  +       KTPIVV D  GF+VNR +  Y++E+  ML +G     I+ A 
Sbjct: 481 DTGDKALAVALDYVAAIRKTPIVVNDTRGFFVNRCVLRYMSESYDMLIEGVPPVMIENAA 540

Query: 524 VKFGFPVGPIQLLDEVGIDTGTKIIPVLEAAYGERFSAPAN---VVSSILNDDRKGRKNG 580
              G PVGP+ L DEV ID   KI+    A  GE+   P +   + S +  + R GRKN 
Sbjct: 541 KMAGMPVGPLALNDEVAIDLSLKILKATVADLGEKAIDPRHMDLISSMVEKEGRFGRKNS 600

Query: 581 RGFYLYGQKGRKSKKQVDPAIYPLIGTQGQGRISAPQVAERCVMLMLNEAVRCVDEQVIR 640
           +GFY Y  K   +KK + P +      +    +    + +R ++ +  EA R V+E ++ 
Sbjct: 601 KGFYDYPPK--PAKKSLWPDLKSFYPQKQADEVDVNVLKQRFLVTIALEAARTVEEGIVT 658

Query: 641 SVRDGDIGAVFGIGFPPFLGGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPCERLVEMGA 700
             R+ D+G++ G GF P+ GG   YID +GA   V + ++LA  YG  F P   L +M A
Sbjct: 659 DPREADVGSILGFGFAPYTGGALSYIDGMGAKAFVELAEKLAGTYGKHFKPTPLLKDMAA 718

Query: 701 RGESFW 706
           +GE+F+
Sbjct: 719 KGETFY 724


Lambda     K      H
   0.319    0.137    0.393 

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: 998
Number of extensions: 47
Number of successful extensions: 6
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: 714
Length of database: 737
Length adjustment: 40
Effective length of query: 674
Effective length of database: 697
Effective search space:   469778
Effective search space used:   469778
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: 55 (25.8 bits)

This GapMind analysis is from Apr 09 2024. 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