Alignments for a candidate for pcaD in Rhizorhabdus wittichii RW1

GapMind for catabolism of small carbon sources

Alignments for a candidate for pcaD in Rhizorhabdus wittichii RW1

Align 3-oxoadipate enol-lactonase (EC 3.1.1.24); 4-carboxymuconolactone decarboxylase (EC 4.1.1.44) (characterized)
to candidate WP_011951914.1 SWIT_RS05450 3-oxoadipate enol-lactonase

Query= BRENDA::Q0SH24
         (400 letters)



>NCBI__GCF_000016765.1:WP_011951914.1
          Length = 397

 Score =  238 bits (606), Expect = 3e-67
 Identities = 137/375 (36%), Positives = 205/375 (54%), Gaps = 5/375 (1%)

Query: 15  GAADAPVVVLLGSLGSNRSMWDPQIAALSYECRVVAVDQRGHGESPAPDGPYSVRDLSED 74
           G+ + P +VLL S+G++ S+WD  +  L    R++ +D RGHG S AP G Y +  L++D
Sbjct: 17  GSDERPPLVLLNSIGTDISLWDRTVPHLLPTFRLLRIDVRGHGASDAPAGDYDLAMLADD 76

Query: 75  VLALLDSLGVDAAHFVGLSMGGAIAQWLGAHAPRRVLSLSLLCTAAKFGEPQAWIERAAA 134
           V A++D  G+  A   G+S+GG IA  +    P +V +L+L+CT+    +P AW  R  A
Sbjct: 77  VAAVMDDAGIAVAPVAGVSLGGMIAMEIALRHPDKVAALALICTSGAM-DPAAWAARVDA 135

Query: 135 SRTDGPESLADAVVARWFSEGLAKRDPEFVRHYREMIASTSPEGYAACCDALADWDFTAD 194
            R  G  ++AD  + R+ S     R PE     +  I + + +GY     A+ D      
Sbjct: 136 VRDGGTGAIADMAIERFLSSDFIVRHPEIAESLKRAIRAQADDGYVGAAAAIRDMALADR 195

Query: 195 LSRISAPTLVIAGEEDPSTP-PSVMQILADGITEARFEVLSPAAHVANLEQAGAVTALLR 253
           +  I+ PTLV+ G  D STP       L   I  A   V++  AH+  +E  G + A ++
Sbjct: 196 IGAIAVPTLVVTGAVDISTPYEGHGDRLVHSIPGAVRAVVA-GAHLPPIEAPGQLAARIQ 254

Query: 254 EHIVG-AGYARGRRAAHAQGMTVRRSILGDAHVDRSVAGTTDFTAPFQDFITRTAWGDIW 312
             ++G A            G+  RR +LGD  VDRS+   T F A FQ  ITR AWG+IW
Sbjct: 255 SFLLGDAAIVEAADTLFEAGLVHRRRVLGDDWVDRSLTKRTAFNADFQALITRIAWGEIW 314

Query: 313 SRPGLDHELRRLLTIAVLTAVGNEHELDMHIRAAL-RAGVDADTIGEVLLHTSVYAGVPN 371
           SRPGLD   RRLL +A+  ++G   E  +H+RA L ++G   D + EVL+ T++YAGVP 
Sbjct: 315 SRPGLDDRTRRLLVVAITASLGCWEEFALHVRAGLGQSGFTRDELKEVLMQTAIYAGVPA 374

Query: 372 SNLGFALGKQALADL 386
           +N  FA  ++ +A+L
Sbjct: 375 ANTAFAEAQRIIAEL 389


Lambda     K      H
   0.318    0.132    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: 442
Number of extensions: 20
Number of successful extensions: 4
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: 400
Length of database: 397
Length adjustment: 31
Effective length of query: 369
Effective length of database: 366
Effective search space:   135054
Effective search space used:   135054
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: 50 (23.9 bits)

Align candidate WP_011951914.1 SWIT_RS05450 (3-oxoadipate enol-lactonase)
to HMM TIGR02427 (pcaD: 3-oxoadipate enol-lactonase (EC 3.1.1.24))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR02427.hmm
# target sequence database:        /tmp/gapView.253013.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02427  [M=251]
Accession:   TIGR02427
Description: protocat_pcaD: 3-oxoadipate enol-lactonase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                             Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    2.1e-82  262.3   0.9    2.8e-82  261.9   0.9    1.2  1  NCBI__GCF_000016765.1:WP_011951914.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000016765.1:WP_011951914.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  261.9   0.9   2.8e-82   2.8e-82       1     250 [.      10     257 ..      10     258 .. 0.99

  Alignments for each domain:
  == domain 1  score: 261.9 bits;  conditional E-value: 2.8e-82
                             TIGR02427   1 rlhyrlegaeadkpvlvlinSLGtdlrlwdkvlealtkdfrvlryDkrGHGlSdvpegpysiedladdvlall 73 
                                           rlh+rl+g++ ++p lvl+nS+Gtd++lwd  +++l + fr+lr+D rGHG+Sd+p+g+y ++ laddv+a++
  NCBI__GCF_000016765.1:WP_011951914.1  10 RLHWRLDGSD-ERPPLVLLNSIGTDISLWDRTVPHLLPTFRLLRIDVRGHGASDAPAGDYDLAMLADDVAAVM 81 
                                           69********.9************************************************************* PP

                             TIGR02427  74 DalgiekaavcGlSlGGliaqaLaarrpdrvealvlsntaakigtaesWeaRiaavraeGlaaladavlerwF 146
                                           D +gi+ a v+G+SlGG+ia+ +a+r+pd+v+al+l++t+  ++    W+aR++avr  G+ a+ad ++er+ 
  NCBI__GCF_000016765.1:WP_011951914.1  82 DDAGIAVAPVAGVSLGGMIAMEIALRHPDKVAALALICTSGAMDP-AAWAARVDAVRDGGTGAIADMAIERFL 153
                                           *******************************************86.89************************* PP

                             TIGR02427 147 tpafreaepaelelvrnmlveqppegYaatcaAirdadlrerleeiavPtlviaGdeDgstPpe.lvreiadl 218
                                           +++f +++p+ +e ++ ++ +q+ +gY++++aAird++l +r+++iavPtlv++G+ D+stP e + ++++++
  NCBI__GCF_000016765.1:WP_011951914.1 154 SSDFIVRHPEIAESLKRAIRAQADDGYVGAAAAIRDMALADRIGAIAVPTLVVTGAVDISTPYEgHGDRLVHS 226
                                           ***************************************************************999******* PP

                             TIGR02427 219 vpgarfaeieeaaHlpnleqpeafaallrdfl 250
                                           +pga  a+++ +aHlp++e+p ++aa++++fl
  NCBI__GCF_000016765.1:WP_011951914.1 227 IPGAVRAVVA-GAHLPPIEAPGQLAARIQSFL 257
                                           **********.*******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (251 nodes)
Target sequences:                          1  (397 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 31.86
//
[ok]

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