GapMind for catabolism of small carbon sources

 

Alignments for a candidate for uxuA in Cronobacter condimenti 1330

Align mannonate dehydratase (EC 4.2.1.8) (characterized)
to candidate WP_007675859.1 BN137_RS06950 mannonate dehydratase

Query= BRENDA::P24215
         (394 letters)



>NCBI__GCF_000319285.1:WP_007675859.1
          Length = 396

 Score =  617 bits (1590), Expect = 0.0
 Identities = 299/392 (76%), Positives = 330/392 (84%)

Query: 1   MEQTWRWYGPNDPVSLADVRQAGATGVVTALHHIPNGEVWSVEEILKRKAIIEDAGLVWS 60
           MEQTWRWYGPNDPVSL D+RQAGATG+VTALHHIPNGEVW VEEI KR+A +   GL WS
Sbjct: 1   MEQTWRWYGPNDPVSLDDIRQAGATGIVTALHHIPNGEVWPVEEIKKRQAELAQKGLTWS 60

Query: 61  VVESVPIHEDIKTHTGNYEQWIANYQQTLRNLAQCGIRTVCYNFMPVLDWTRTDLEYVLP 120
           VVES+P+HEDIKTHTG Y+ +IA YQQ++RNLA CGI TVCYNFMP+LDWTRTDLEY LP
Sbjct: 61  VVESIPVHEDIKTHTGEYDLYIARYQQSIRNLAVCGIDTVCYNFMPILDWTRTDLEYTLP 120

Query: 121 DGSKALRFDQIEFAAFEMHILKRPGAEADYTEEEIAQAAERFATMSDEDKARLTRNIIAG 180
           DGSKALRFDQI FAAFE+HILKR GA  DYTE+E  QA + F  MS+     LTRNIIAG
Sbjct: 121 DGSKALRFDQIAFAAFELHILKRDGARNDYTEDEQRQAQDYFHAMSEAQIETLTRNIIAG 180

Query: 181 LPGAEEGYTLDQFRKHLELYKDIDKAKLRENFAVFLKAIIPVAEEVGVRMAVHPDDPPRP 240
           LPGAEEGYTLDQFR  L  Y  IDKA LREN A FLKAI+PVAEE GVR+AVHPDDPPRP
Sbjct: 181 LPGAEEGYTLDQFRARLAEYDPIDKAALRENMAYFLKAIVPVAEEAGVRLAVHPDDPPRP 240

Query: 241 ILGLPRIVSTIEDMQWMVDTVNSMANGFTMCTGSYGVRADNDLVDMIKQFGPRIYFTHLR 300
           ILGLPRIVSTIEDM W+ +TV+S+ NGFTMCTGSYGVRADNDLV M++ F  RI+FTHLR
Sbjct: 241 ILGLPRIVSTIEDMLWLKETVDSIYNGFTMCTGSYGVRADNDLVRMVETFADRIHFTHLR 300

Query: 301 STMREDNPKTFHEAAHLNGDVDMYEVVKAIVEEEHRRKAEGKEDLIPMRPDHGHQMLDDL 360
           +T RE NPKTFHEAAHL GDVDM  VVKAI+ EE RRK  G    IP RPDHGHQMLDDL
Sbjct: 301 ATCREANPKTFHEAAHLYGDVDMVAVVKAILTEEQRRKKAGDLRPIPFRPDHGHQMLDDL 360

Query: 361 KKKTNPGYSAIGRLKGLAEVRGVELAIQRAFF 392
           +KKTNPGYSAIGRLKGLAEVRG+ELA+++  F
Sbjct: 361 RKKTNPGYSAIGRLKGLAEVRGIELALKKVLF 392


Lambda     K      H
   0.320    0.136    0.410 

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: 594
Number of extensions: 22
Number of successful extensions: 1
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: 394
Length of database: 396
Length adjustment: 31
Effective length of query: 363
Effective length of database: 365
Effective search space:   132495
Effective search space used:   132495
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_007675859.1 BN137_RS06950 (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.3410037.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   7.9e-210  682.8   0.0   8.9e-210  682.6   0.0    1.0  1  NCBI__GCF_000319285.1:WP_007675859.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000319285.1:WP_007675859.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  682.6   0.0  8.9e-210  8.9e-210       1     392 [.       1     392 [.       1     394 [. 1.00

  Alignments for each domain:
  == domain 1  score: 682.6 bits;  conditional E-value: 8.9e-210
                             TIGR00695   1 meqtfrwyGrndpvsledvrqaGakGivtalhhipnGevweveeikkrkeeiedaGlsasvvesvpvheeikl 73 
                                           meqt+rwyG+ndpvsl+d+rqaGa+GivtalhhipnGevw veeikkr++e+ + Gl++svves+pvhe+ik+
  NCBI__GCF_000319285.1:WP_007675859.1   1 MEQTWRWYGPNDPVSLDDIRQAGATGIVTALHHIPNGEVWPVEEIKKRQAELAQKGLTWSVVESIPVHEDIKT 73 
                                           9************************************************************************ PP

                             TIGR00695  74 qteeyekyienykqtlrnlaqcGikvvcynfmpvldwtrtdlayeledGskalrfdkikvaalelhilkrpda 146
                                           +t+ey+ yi+ y+q++rnla cGi++vcynfmp+ldwtrtdl+y+l+dGskalrfd+i++aa+elhilkr +a
  NCBI__GCF_000319285.1:WP_007675859.1  74 HTGEYDLYIARYQQSIRNLAVCGIDTVCYNFMPILDWTRTDLEYTLPDGSKALRFDQIAFAAFELHILKRDGA 146
                                           ************************************************************************* PP

                             TIGR00695 147 ekdyteeelvraveeasdmseedkarltrniiaglpGaeegekldrikelleaykdideeklrenlafflkei 219
                                            +dyte+e+ +a+++++ mse ++  ltrniiaglpGaeeg++ld+++ +l+ y  id++ lren+a+flk+i
  NCBI__GCF_000319285.1:WP_007675859.1 147 RNDYTEDEQRQAQDYFHAMSEAQIETLTRNIIAGLPGAEEGYTLDQFRARLAEYDPIDKAALRENMAYFLKAI 219
                                           ************************************************************************* PP

                             TIGR00695 220 lpvaeevGvkmaihpddpprpilGlprivstiedmkklveisdspangitlctGsyGvradndlvelakqfad 292
                                           +pvaee Gv++a+hpddpprpilGlprivstiedm +l+e++ds  ng+t+ctGsyGvradndlv ++++fad
  NCBI__GCF_000319285.1:WP_007675859.1 220 VPVAEEAGVRLAVHPDDPPRPILGLPRIVSTIEDMLWLKETVDSIYNGFTMCTGSYGVRADNDLVRMVETFAD 292
                                           ************************************************************************* PP

                             TIGR00695 293 riyfahlrsvkreenpktfheaahlekdvdlyevvkavleeehrrkaeGkedlipvrpdhGrqllddlkkktn 365
                                           ri+f+hlr++ re npktfheaahl +dvd+  vvka+l ee rrk+ G+ + ip rpdhG+q+lddl+kktn
  NCBI__GCF_000319285.1:WP_007675859.1 293 RIHFTHLRATCREANPKTFHEAAHLYGDVDMVAVVKAILTEEQRRKKAGDLRPIPFRPDHGHQMLDDLRKKTN 365
                                           ************************************************************************* PP

                             TIGR00695 366 pGysaigrlkGlaelrGlelalkkvaf 392
                                           pGysaigrlkGlae+rG+elalkkv f
  NCBI__GCF_000319285.1:WP_007675859.1 366 PGYSAIGRLKGLAEVRGIELALKKVLF 392
                                           ************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (394 nodes)
Target sequences:                          1  (396 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: 20.86
//
[ok]

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:

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:

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:

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:

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