Alignments for a candidate for uxuA in Pedobacter sp. GW460-11-11-14-LB5

GapMind for catabolism of small carbon sources

Alignments for a candidate for uxuA in Pedobacter sp. GW460-11-11-14-LB5

Align mannonate dehydratase (EC 4.2.1.8) (characterized)
to candidate CA265_RS07225 CA265_RS07225 mannonate dehydratase

Query= BRENDA::P24215
         (394 letters)



>FitnessBrowser__Pedo557:CA265_RS07225
          Length = 389

 Score =  429 bits (1103), Expect = e-125
 Identities = 208/387 (53%), Positives = 278/387 (71%), Gaps = 7/387 (1%)

Query: 1   MEQTWRWYGPNDPVSLADVRQAGATGVVTALHHIPNGEVWSVEEILKRKAIIEDAGLVWS 60
           +EQTWRWYGPNDPVSL DV+QAGATG+VTALHHIP+GEVW + +I +RKAIIE AGL WS
Sbjct: 6   LEQTWRWYGPNDPVSLQDVKQAGATGIVTALHHIPHGEVWPLTDIQERKAIIEAAGLTWS 65

Query: 61  VVESVPIHEDIKTHTGNYEQWIANYQQTLRNLAQCGIRTVCYNFMPVLDWTRTDLEYVLP 120
           VVESVP+HE IKT   +  ++I NY+ +LRNL+ CGI+ VCYNFMPVLDWTRT L+  + 
Sbjct: 66  VVESVPVHEAIKTRRADAGKYIENYKTSLRNLSACGIKIVCYNFMPVLDWTRTQLDLEMT 125

Query: 121 DGSKALRFDQIEFAAFEMHILKRPGAEADYTEEEIAQAAERFATMSDEDKARLTRNIIAG 180
           DGSKAL F+ I+ A F+++ILKR GAEADY++  + +A  +++T++++D A L  N++ G
Sbjct: 126 DGSKALYFNWIDLAIFDLYILKREGAEADYSKSILDRAEAKYSTLTEQDLADLRVNVLMG 185

Query: 181 LPGAEEGYTLDQFRKHLELYKDIDKAKLRENFAVFLKAIIPVAEEVGVRMAVHPDDPPRP 240
           +P  +E   L+  R  +  YK I    L+EN   FL +I  V    G++M +HPDDPP  
Sbjct: 186 IPNEKE-IELETLRNSINEYKAIGTQGLKENLKFFLSSIAEVCTTEGIKMTIHPDDPPYA 244

Query: 241 ILGLPRIVSTIEDMQWMVDTVNSMANGFTMCTGSYGVRADNDLVDMIKQFGPRIYFTHLR 300
           ILGLPRI ST+ED  +++  V+   NG   CTGS G    N+ +++      R+YF HLR
Sbjct: 245 ILGLPRIASTLEDFNYIIKEVDQAFNGVCFCTGSLGAGMGNNALEIFNAVKERVYFAHLR 304

Query: 301 STMREDNPKTFHEAAHLNGDVDMYEVVKAIVEEEHRRKAEGKEDLIPMRPDHGHQMLDDL 360
           + +++D   +F+EA HL GDV+MYE++KA+ EE   R     +  IP RPDHGHQMLDDL
Sbjct: 305 N-VKKDEDGSFYEADHLGGDVNMYEIMKALSEENALR-----DKSIPFRPDHGHQMLDDL 358

Query: 361 KKKTNPGYSAIGRLKGLAEVRGVELAI 387
            K TNPGYSAIGRL+GLAE+RG+E+ +
Sbjct: 359 AKVTNPGYSAIGRLRGLAELRGLEIGV 385


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: 476
Number of extensions: 14
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 CA265_RS07225 CA265_RS07225 (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.22556.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   3.5e-155  502.9   0.0     4e-155  502.7   0.0    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS07225  CA265_RS07225 mannonate dehydrat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS07225  CA265_RS07225 mannonate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  502.7   0.0    4e-155    4e-155       1     387 [.       6     385 ..       6     389 .] 0.98

  Alignments for each domain:
  == domain 1  score: 502.7 bits;  conditional E-value: 4e-155
                                  TIGR00695   1 meqtfrwyGrndpvsledvrqaGakGivtalhhipnGevweveeikkrkeeiedaGlsasvvesvpvh 68 
                                                +eqt+rwyG+ndpvsl+dv+qaGa+Givtalhhip Gevw   +i++rk++ie aGl++svvesvpvh
  lcl|FitnessBrowser__Pedo557:CA265_RS07225   6 LEQTWRWYGPNDPVSLQDVKQAGATGIVTALHHIPHGEVWPLTDIQERKAIIEAAGLTWSVVESVPVH 73 
                                                59****************************************************************** PP

                                  TIGR00695  69 eeiklqteeyekyienykqtlrnlaqcGikvvcynfmpvldwtrtdlayeledGskalrfdkikvaal 136
                                                e+ik++  + +kyienyk +lrnl+ cGik+vcynfmpvldwtrt+l  e+ dGskal+f+ i++a +
  lcl|FitnessBrowser__Pedo557:CA265_RS07225  74 EAIKTRRADAGKYIENYKTSLRNLSACGIKIVCYNFMPVLDWTRTQLDLEMTDGSKALYFNWIDLAIF 141
                                                ******************************************************************** PP

                                  TIGR00695 137 elhilkrpdaekdyteeelvraveeasdmseedkarltrniiaglpGaeegekldrikelleaykdid 204
                                                +l+ilkr +ae+dy++  l ra  ++s+++e+d a l  n++ g+p  +e  +l+ +++ ++ yk i 
  lcl|FitnessBrowser__Pedo557:CA265_RS07225 142 DLYILKREGAEADYSKSILDRAEAKYSTLTEQDLADLRVNVLMGIPNEKE-IELETLRNSINEYKAIG 208
                                                **********************************************9888.99*************** PP

                                  TIGR00695 205 eeklrenlafflkeilpvaeevGvkmaihpddpprpilGlprivstiedmkklveisdspangitlct 272
                                                 + l+enl ffl  i  v    G+km+ihpddpp+ ilGlpri st ed++++++ +d   ng+ +ct
  lcl|FitnessBrowser__Pedo557:CA265_RS07225 209 TQGLKENLKFFLSSIAEVCTTEGIKMTIHPDDPPYAILGLPRIASTLEDFNYIIKEVDQAFNGVCFCT 276
                                                ******************************************************************** PP

                                  TIGR00695 273 GsyGvradndlvelakqfadriyfahlrsvkreenpktfheaahlekdvdlyevvkavleeehrrkae 340
                                                Gs+G+   n+ +e+ +   +r+yfahlr+vk++e++ +f+ea hl +dv++ye++ka+ ee+  r++ 
  lcl|FitnessBrowser__Pedo557:CA265_RS07225 277 GSLGAGMGNNALEIFNAVKERVYFAHLRNVKKDEDG-SFYEADHLGGDVNMYEIMKALSEENALRDKS 343
                                                ************************************.9**********************99888764 PP

                                  TIGR00695 341 GkedlipvrpdhGrqllddlkkktnpGysaigrlkGlaelrGlelal 387
                                                     ip rpdhG+q+lddl k tnpGysaigrl+GlaelrGle+ +
  lcl|FitnessBrowser__Pedo557:CA265_RS07225 344 -----IPFRPDHGHQMLDDLAKVTNPGYSAIGRLRGLAELRGLEIGV 385
                                                .....7*************************************9865 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 8.09
//
[ok]

This GapMind analysis is from Sep 17 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 paper from 2022 on GapMind for carbon sources, or view the source code.

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