Alignments for a candidate for uxuA in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for uxuA in Azospirillum brasilense Sp245

Align mannonate dehydratase (EC 4.2.1.8) (characterized)
to candidate AZOBR_RS31370 AZOBR_RS31370 mannonate dehydratase

Query= BRENDA::Q1QT83
         (391 letters)



>FitnessBrowser__azobra:AZOBR_RS31370
          Length = 398

 Score =  449 bits (1155), Expect = e-131
 Identities = 222/394 (56%), Positives = 280/394 (71%), Gaps = 6/394 (1%)

Query: 1   MEHTWRWFGPDDPITLDEIRQTGATGIVTALHEIPNGEIWPEAAIAERKRLIEAS---GL 57
           ME TWRWFGPDD I L+ IRQTGATGIVTALH+IP G +W    I ERK +I A    GL
Sbjct: 1   MEQTWRWFGPDDVIRLNHIRQTGATGIVTALHQIPYGVVWSVEEIEERKAMIAADPSLGL 60

Query: 58  AWSVVESVPVHEDIKQGRGDCETHIARYQQTLRNLAACGIDVVCYNFMPVLDWTRTDLAW 117
            WSVVES+PVHE IK G GD       Y+Q+LRNLAACG+  VCYNFMP+LDWTRTDLA 
Sbjct: 61  RWSVVESLPVHESIKIGEGDLAPLFDNYRQSLRNLAACGVTTVCYNFMPILDWTRTDLAA 120

Query: 118 PLPGGGTALRFDQTAFAAFDLYLLERPGAEADYDATERDAARAYLDGLDESARQRLIDTI 177
           P+PGGGT+LRF+    AAFD+++LERPGAE D+       ARA+ D   E  ++ L+  I
Sbjct: 121 PVPGGGTSLRFNAHEHAAFDVFMLERPGAEDDHSPEVLARARAWFDKASEDDKKTLLANI 180

Query: 178 IAGLPGAEEHYSLARFREVIAEYAEIDAERLRDNLGHFLRAVVPVAEEVGIRLAIHPDDP 237
           +AGLPGA + Y +   R+++  Y ++    LR+ L  FLR V+P AEEVGIR+ IHPDDP
Sbjct: 181 MAGLPGAFDRYDIPGLRKMLDRYKDMSHGALRETLARFLREVIPTAEEVGIRMCIHPDDP 240

Query: 238 PRPLLGLPRVVSTPRDVQWILDAAPSPANGLTFCTGSYGVSAAIDLVAMGERFAERIYFA 297
           PRPL+GLPR+VS   D+ +I++   S ANG+TFCTGS G  A  D+ AM +RFA ++ FA
Sbjct: 241 PRPLMGLPRIVSNEDDLDFIVNVIDSEANGITFCTGSLGAGAKNDVPAMIKRFAPKVTFA 300

Query: 298 HLRATQRENDPRSFHESAHLDGDVDMVGVIKALVGEERRRERDGGP--RLPLRPDHGHHL 355
           HLR  +++ D  SF E+ HL GDVDMV V+  L+ E++RR+  G P  R+P RPDHGH L
Sbjct: 301 HLRNVKKDPD-GSFQEAEHLGGDVDMVSVVTTLLEEQKRRKDAGNPNWRIPFRPDHGHEL 359

Query: 356 LDDLSRDTRPGYPLIGRLKGLAELRGVETAIKQL 389
           LDD+ + T PGYP IGRL+GLAE+RGV TA+  +
Sbjct: 360 LDDVGKKTHPGYPAIGRLRGLAEIRGVMTAVASM 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: 488
Number of extensions: 23
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 AZOBR_RS31370 AZOBR_RS31370 (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.31535.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.3e-158  512.9   0.0     4e-158  512.6   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS31370  AZOBR_RS31370 mannonate dehydrat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS31370  AZOBR_RS31370 mannonate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  512.6   0.0    4e-158    4e-158       1     390 [.       1     393 [.       1     395 [. 0.98

  Alignments for each domain:
  == domain 1  score: 512.6 bits;  conditional E-value: 4e-158
                                 TIGR00695   1 meqtfrwyGrndpvsledvrqaGakGivtalhhipnGevweveeikkrkeeie...daGlsasvvesvp 66 
                                               meqt+rw+G++d + l+++rq Ga+Givtalh+ip G vw+veei++rk++i    + Gl +svves+p
  lcl|FitnessBrowser__azobra:AZOBR_RS31370   1 MEQTWRWFGPDDVIRLNHIRQTGATGIVTALHQIPYGVVWSVEEIEERKAMIAadpSLGLRWSVVESLP 69 
                                               9***************************************************744468*********** PP

                                 TIGR00695  67 vheeiklqteeyekyienykqtlrnlaqcGikvvcynfmpvldwtrtdlayeledGskalrfdkikvaa 135
                                               vhe ik+++++     +ny+q+lrnla cG+ +vcynfmp+ldwtrtdla +++ G ++lrf+  + aa
  lcl|FitnessBrowser__azobra:AZOBR_RS31370  70 VHESIKIGEGDLAPLFDNYRQSLRNLAACGVTTVCYNFMPILDWTRTDLAAPVPGGGTSLRFNAHEHAA 138
                                               ********************************************************************* PP

                                 TIGR00695 136 lelhilkrpdaekdyteeelvraveeasdmseedkarltrniiaglpGaeegekldrikelleaykdid 204
                                               +++++l+rp+ae d++ e l+ra+  +++ se+dk  l  ni+aglpGa + + +  +++ l++ykd++
  lcl|FitnessBrowser__azobra:AZOBR_RS31370 139 FDVFMLERPGAEDDHSPEVLARARAWFDKASEDDKKTLLANIMAGLPGAFDRYDIPGLRKMLDRYKDMS 207
                                               ********************************************************************* PP

                                 TIGR00695 205 eeklrenlafflkeilpvaeevGvkmaihpddpprpilGlprivstiedmkklveisdspangitlctG 273
                                               +  lre la fl+e++p aeevG++m ihpddpprp++Glprivs ++d+  +v++ ds angit+ctG
  lcl|FitnessBrowser__azobra:AZOBR_RS31370 208 HGALRETLARFLREVIPTAEEVGIRMCIHPDDPPRPLMGLPRIVSNEDDLDFIVNVIDSEANGITFCTG 276
                                               ********************************************************************* PP

                                 TIGR00695 274 syGvradndlvelakqfadriyfahlrsvkreenpktfheaahlekdvdlyevvkavleeehrrkaeGk 342
                                               s+G+ a+nd+  ++k+fa+++ fahlr+vk++ ++ +f+ea hl +dvd+  vv ++lee+ rrk  G+
  lcl|FitnessBrowser__azobra:AZOBR_RS31370 277 SLGAGAKNDVPAMIKRFAPKVTFAHLRNVKKDPDG-SFQEAEHLGGDVDMVSVVTTLLEEQKRRKDAGN 344
                                               ********************************999.9*******************************9 PP

                                 TIGR00695 343 ed.lipvrpdhGrqllddlkkktnpGysaigrlkGlaelrGlelalkkv 390
                                                +  ip rpdhG++lldd+ kkt+pGy aigrl+Glae+rG+ +a+  +
  lcl|FitnessBrowser__azobra:AZOBR_RS31370 345 PNwRIPFRPDHGHELLDDVGKKTHPGYPAIGRLRGLAEIRGVMTAVASM 393
                                               76369***************************************99776 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: 00:00:00.01
# Mc/sec: 10.43
//
[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
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