Alignments for a candidate for uxuA in Methylobacterium nodulans ORS 2060

GapMind for catabolism of small carbon sources

Alignments for a candidate for uxuA in Methylobacterium nodulans ORS 2060

Align mannonate dehydratase (EC 4.2.1.8) (characterized)
to candidate WP_015927688.1 MNOD_RS04710 mannonate dehydratase

Query= BRENDA::Q1QT83
         (391 letters)



>NCBI__GCF_000022085.1:WP_015927688.1
          Length = 398

 Score =  444 bits (1142), Expect = e-129
 Identities = 228/394 (57%), Positives = 272/394 (69%), Gaps = 6/394 (1%)

Query: 1   MEHTWRWFGPDDPITLDEIRQTGATGIVTALHEIPNGEIWPEAAIAERKRLIEAS---GL 57
           ME TWRWFGPDD + L + RQ GATGIVTALH IP GE+W  A I  RK  I A    GL
Sbjct: 1   MEQTWRWFGPDDCVRLADARQAGATGIVTALHHIPYGEVWSIAEIERRKAEIGADPSLGL 60

Query: 58  AWSVVESVPVHEDIKQGRGDCETHIARYQQTLRNLAACGIDVVCYNFMPVLDWTRTDLAW 117
            WSVVES+PVHE IK G GD E   A Y+ +LRNLAACGI  +CYNFMPVLDWTRT+LA 
Sbjct: 61  RWSVVESLPVHERIKLGEGDLEPLFAAYRASLRNLAACGITTICYNFMPVLDWTRTELAH 120

Query: 118 PLPGGGTALRFDQTAFAAFDLYLLERPGAEADYDATERDAARAYLDGLDESARQRLIDTI 177
           PLPGGGTALRF+   FAAFD ++L RPGAEAD+        RA+     E+ R +L+ TI
Sbjct: 121 PLPGGGTALRFNAHEFAAFDCFMLARPGAEADHPPEALARGRAWFTRSSEADRAKLLATI 180

Query: 178 IAGLPGAEEHYSLARFREVIAEYAEIDAERLRDNLGHFLRAVVPVAEEVGIRLAIHPDDP 237
           +AGLPGA + Y +A  R ++  Y  ID   LR NL  FLRAV+P A EVGIR+AIHPDDP
Sbjct: 181 MAGLPGAFDRYDIAGLRRMLDRYRGIDTNTLRGNLAAFLRAVIPTAAEVGIRMAIHPDDP 240

Query: 238 PRPLLGLPRVVSTPRDVQWILDAAPSPANGLTFCTGSYGVSAAIDLVAMGERFAERIYFA 297
           PRPL+GLPR+VS   D+ +I  A  + ANG+T C+GS G   A D+ A+  RFA RI+FA
Sbjct: 241 PRPLMGLPRIVSNADDLAFITGAVDAEANGITLCSGSLGAGPANDVPALARRFAHRIHFA 300

Query: 298 HLRATQRENDPRSFHESAHLDGDVDMVGVIKALVGEERRRERDGGP--RLPLRPDHGHHL 355
           HLR   +E D  SF E+ HL GD DMV +I AL+ E+ RR   G P  R+P+RPDHGH L
Sbjct: 301 HLRNVAKEPD-GSFMEADHLGGDTDMVALIDALLAEQERRRAAGDPRWRIPMRPDHGHAL 359

Query: 356 LDDLSRDTRPGYPLIGRLKGLAELRGVETAIKQL 389
           L D+ +   PGY  +GRLKGLAELRGV TA+  L
Sbjct: 360 LSDIGQGAFPGYTAVGRLKGLAELRGVMTALASL 393


Lambda     K      H
   0.321    0.139    0.430 

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: 476
Number of extensions: 21
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: 391
Length of database: 398
Length adjustment: 31
Effective length of query: 360
Effective length of database: 367
Effective search space:   132120
Effective search space used:   132120
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: 50 (23.9 bits)

Align candidate WP_015927688.1 MNOD_RS04710 (mannonate dehydratase)
to HMM TIGR00695 (uxuA: mannonate dehydratase (EC 4.2.1.8))

# 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/TIGR00695.hmm
# target sequence database:        /tmp/gapView.572705.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00695  [M=394]
Accession:   TIGR00695
Description: uxuA: mannonate dehydratase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.1e-152  492.5   0.0   6.2e-152  492.2   0.0    1.0  1  NCBI__GCF_000022085.1:WP_015927688.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000022085.1:WP_015927688.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  492.2   0.0  6.2e-152  6.2e-152       1     388 [.       1     391 [.       1     394 [. 0.98

  Alignments for each domain:
  == domain 1  score: 492.2 bits;  conditional E-value: 6.2e-152
                             TIGR00695   1 meqtfrwyGrndpvsledvrqaGakGivtalhhipnGevweveeikkrkeeie...daGlsasvvesvpvhee 70 
                                           meqt+rw+G++d v l+d rqaGa+Givtalhhip Gevw++ ei++rk+ei    + Gl +svves+pvhe 
  NCBI__GCF_000022085.1:WP_015927688.1   1 MEQTWRWFGPDDCVRLADARQAGATGIVTALHHIPYGEVWSIAEIERRKAEIGadpSLGLRWSVVESLPVHER 73 
                                           9***************************************************633468*************** PP

                             TIGR00695  71 iklqteeyekyienykqtlrnlaqcGikvvcynfmpvldwtrtdlayeledGskalrfdkikvaalelhilkr 143
                                           ikl++++ e   + y+ +lrnla cGi ++cynfmpvldwtrt+la++l+ G +alrf+  ++aa++ ++l r
  NCBI__GCF_000022085.1:WP_015927688.1  74 IKLGEGDLEPLFAAYRASLRNLAACGITTICYNFMPVLDWTRTELAHPLPGGGTALRFNAHEFAAFDCFMLAR 146
                                           ************************************************************************* PP

                             TIGR00695 144 pdaekdyteeelvraveeasdmseedkarltrniiaglpGaeegekldrikelleaykdideeklrenlaffl 216
                                           p+ae+d+  e l+r +  ++  se d+a+l   i+aglpGa + + ++ +++ l++y+ id + lr nla fl
  NCBI__GCF_000022085.1:WP_015927688.1 147 PGAEADHPPEALARGRAWFTRSSEADRAKLLATIMAGLPGAFDRYDIAGLRRMLDRYRGIDTNTLRGNLAAFL 219
                                           ************************************************************************* PP

                             TIGR00695 217 keilpvaeevGvkmaihpddpprpilGlprivstiedmkklveisdspangitlctGsyGvradndlvelakq 289
                                           ++++p a evG++maihpddpprp++Glprivs  +d+  +   +d+ angitlc+Gs+G+ ++nd+  la++
  NCBI__GCF_000022085.1:WP_015927688.1 220 RAVIPTAAEVGIRMAIHPDDPPRPLMGLPRIVSNADDLAFITGAVDAEANGITLCSGSLGAGPANDVPALARR 292
                                           ************************************************************************* PP

                             TIGR00695 290 fadriyfahlrsvkreenpktfheaahlekdvdlyevvkavleeehrrkaeGked.lipvrpdhGrqllddlk 361
                                           fa+ri+fahlr+v +e ++ +f+ea hl +d+d+  ++ a+l e+ rr+a G+ +  ip+rpdhG+ ll d+ 
  NCBI__GCF_000022085.1:WP_015927688.1 293 FAHRIHFAHLRNVAKEPDG-SFMEADHLGGDTDMVALIDALLAEQERRRAAGDPRwRIPMRPDHGHALLSDIG 364
                                           *******************.9*******************************987359*************** PP

                             TIGR00695 362 kktnpGysaigrlkGlaelrGlelalk 388
                                           + + pGy+a+grlkGlaelrG+ +al 
  NCBI__GCF_000022085.1:WP_015927688.1 365 QGAFPGYTAVGRLKGLAELRGVMTALA 391
                                           ***********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (394 nodes)
Target sequences:                          1  (398 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 17.45
//
[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