Alignments for a candidate for uxuA in Leeuwenhoekiella blandensis MED217

GapMind for catabolism of small carbon sources

Alignments for a candidate for uxuA in Leeuwenhoekiella blandensis MED217

Align mannonate dehydratase (EC 4.2.1.8) (characterized)
to candidate WP_009779324.1 MED217_RS04640 mannonate dehydratase

Query= BRENDA::P24215
         (394 letters)



>NCBI__GCF_000152985.1:WP_009779324.1
          Length = 389

 Score =  411 bits (1056), Expect = e-119
 Identities = 214/389 (55%), Positives = 271/389 (69%), Gaps = 7/389 (1%)

Query: 1   MEQTWRWYGPNDPVSLADVRQAGATGVVTALHHIPNGEVWSVEEILKRKAIIEDAGLVWS 60
           M QT RWYG  D V+L D+RQAGATGVV A+H I NGEVWS+E + +RK  IE AGL W 
Sbjct: 1   MIQTMRWYGHKDLVTLQDIRQAGATGVVHAMHEITNGEVWSLEALQQRKQEIEAAGLDWK 60

Query: 61  VVESVPIHEDIKTHTGNYEQWIANYQQTLRNLAQCGIRTVCYNFMPVLDWTRTDLEYVLP 120
           VVES+P+ E IKT +G++++ I NY+Q+L NL + G+  VCYNFMPVLDWTRT L Y L 
Sbjct: 61  VVESLPVTEPIKTRSGDFQKHIDNYKQSLINLGKIGVEVVCYNFMPVLDWTRTQLAYPLE 120

Query: 121 DGSKALRFDQIEFAAFEMHILKRPGAEADYTEEEIAQAAERFATMSDEDKARLTRNIIAG 180
           +G+ ALRFD    AAF+  +LKR  AE +Y+E  +A+A   F + + E+K +L   IIAG
Sbjct: 121 NGATALRFDWAHLAAFDCFMLKRKDAEKEYSEAILAEAKHFFESATTEEKQQLENAIIAG 180

Query: 181 LPGAEEGYTLDQFRKHLELYKDIDKAKLRENFAVFLKAIIPVAEEVGVRMAVHPDDPPRP 240
           LPGAEEGY L   +  ++ Y  ID+ + +E+  +FL  IIPVAE  G+ MA+HPDDPP P
Sbjct: 181 LPGAEEGYDLQGLQTAIDKYAAIDEIQAQEHLKLFLNEIIPVAETAGIAMAIHPDDPPHP 240

Query: 241 ILGLPRIVSTIEDMQWMVDTVNSMANGFTMCTGSYGVRADNDLVDMIKQFGPRIYFTHLR 300
             GLPRI+S   D++ +++   S  NG T CTGS+G RADNDLV MI  +G  I+F HLR
Sbjct: 241 FFGLPRIMSKASDIKRLLEDNASAFNGVTFCTGSFGARADNDLVQMINDYGSHIHFIHLR 300

Query: 301 STMREDNPKTFHEAAHLNGDVDMYEVVKAIVEEEHRRKAEGKEDLIPMRPDHGHQMLDDL 360
           ST R D    F E  HL GDV M  VV A++E E   K+ GK+  +PMRPDHGHQMLDDL
Sbjct: 301 STKR-DATGNFFEDNHLEGDVPMPAVVHALLEVE---KSRGKQ--LPMRPDHGHQMLDDL 354

Query: 361 KKK-TNPGYSAIGRLKGLAEVRGVELAIQ 388
           KK   +PGY+AIGRLKGLAE+RGV   I+
Sbjct: 355 KKPLAHPGYTAIGRLKGLAELRGVIAGIE 383


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: 480
Number of extensions: 24
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: 394
Length of database: 389
Length adjustment: 31
Effective length of query: 363
Effective length of database: 358
Effective search space:   129954
Effective search space used:   129954
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_009779324.1 MED217_RS04640 (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.1291356.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.1e-157  509.7   0.0   3.4e-157  509.5   0.0    1.0  1  NCBI__GCF_000152985.1:WP_009779324.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000152985.1:WP_009779324.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  509.5   0.0  3.4e-157  3.4e-157       1     391 [.       1     386 [.       1     389 [] 0.98

  Alignments for each domain:
  == domain 1  score: 509.5 bits;  conditional E-value: 3.4e-157
                             TIGR00695   1 meqtfrwyGrndpvsledvrqaGakGivtalhhipnGevweveeikkrkeeiedaGlsasvvesvpvheeikl 73 
                                           m qt+rwyG++d v+l+d+rqaGa+G+v a+h+i nGevw+ e +++rk+eie aGl ++vves+pv e ik+
  NCBI__GCF_000152985.1:WP_009779324.1   1 MIQTMRWYGHKDLVTLQDIRQAGATGVVHAMHEITNGEVWSLEALQQRKQEIEAAGLDWKVVESLPVTEPIKT 73 
                                           779********************************************************************** PP

                             TIGR00695  74 qteeyekyienykqtlrnlaqcGikvvcynfmpvldwtrtdlayeledGskalrfdkikvaalelhilkrpda 146
                                           ++++++k+i+nykq+l nl ++G++vvcynfmpvldwtrt+lay+le+G++alrfd +++aa++ ++lkr da
  NCBI__GCF_000152985.1:WP_009779324.1  74 RSGDFQKHIDNYKQSLINLGKIGVEVVCYNFMPVLDWTRTQLAYPLENGATALRFDWAHLAAFDCFMLKRKDA 146
                                           ************************************************************************* PP

                             TIGR00695 147 ekdyteeelvraveeasdmseedkarltrniiaglpGaeegekldrikelleaykdideeklrenlafflkei 219
                                           ek+y+e  l++a++ +++ + e+k +l   iiaglpGaeeg+ l+ +++ +++y  ide + +e+l +fl+ei
  NCBI__GCF_000152985.1:WP_009779324.1 147 EKEYSEAILAEAKHFFESATTEEKQQLENAIIAGLPGAEEGYDLQGLQTAIDKYAAIDEIQAQEHLKLFLNEI 219
                                           ************************************************************************* PP

                             TIGR00695 220 lpvaeevGvkmaihpddpprpilGlprivstiedmkklveisdspangitlctGsyGvradndlvelakqfad 292
                                           +pvae  G+ maihpddpp+p +Glpri+s   d+k+l e + s  ng+t+ctGs+G+radndlv++++ +++
  NCBI__GCF_000152985.1:WP_009779324.1 220 IPVAETAGIAMAIHPDDPPHPFFGLPRIMSKASDIKRLLEDNASAFNGVTFCTGSFGARADNDLVQMINDYGS 292
                                           ************************************************************************* PP

                             TIGR00695 293 riyfahlrsvkreenpktfheaahlekdvdlyevvkavleeehrrkaeGkedlipvrpdhGrqllddlkkk.t 364
                                            i+f hlrs+kr+  + +f+e  hle+dv +  vv+a+le e  r ++     +p+rpdhG+q+lddlkk  +
  NCBI__GCF_000152985.1:WP_009779324.1 293 HIHFIHLRSTKRDATG-NFFEDNHLEGDVPMPAVVHALLEVEKSRGKQ-----LPMRPDHGHQMLDDLKKPlA 359
                                           *************999.9*********************998766554.....6**************99637 PP

                             TIGR00695 365 npGysaigrlkGlaelrGlelalkkva 391
                                           +pGy+aigrlkGlaelrG+   ++ + 
  NCBI__GCF_000152985.1:WP_009779324.1 360 HPGYTAIGRLKGLAELRGVIAGIEFMQ 386
                                           9******************99988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (394 nodes)
Target sequences:                          1  (389 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: 21.27
//
[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:

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