GapMind for catabolism of small carbon sources

 

Alignments for a candidate for 1pfk in Azospirillum brasilense Sp245

Align 1-phosphofructokinase (EC 2.7.1.56) (characterized)
to candidate AZOBR_RS30840 AZOBR_RS30840 hypothetical protein

Query= reanno::psRCH2:GFF3290
         (312 letters)



>FitnessBrowser__azobra:AZOBR_RS30840
          Length = 323

 Score =  209 bits (531), Expect = 9e-59
 Identities = 128/313 (40%), Positives = 175/313 (55%), Gaps = 6/313 (1%)

Query: 4   VLTVTLNPALDLTVQLPALRLGEVNRSDSLQVHAAGKGLNVAQVLADLG-----HQLTVT 58
           V+TVTLN A+D T+ +P    G VNR+ +    A GKG+NVA  LA          +T T
Sbjct: 11  VVTVTLNAAIDQTLDVPGFAAGAVNRAVAETRTAGGKGINVAAFLAGASLAGGATPVTAT 70

Query: 59  GFLGEGNPQAFEQLFSARGFTDEFVRVAGETRSNLKLAEADGR-VTDINGPGLAVSEAQR 117
           GFLGE N   F+ LF  RG  D  +R+AG +R N+KL + +G  VTDIN PGL V     
Sbjct: 71  GFLGEENTAVFDALFRRRGIRDRCLRLAGRSRVNIKLVDREGHSVTDINLPGLHVPAESW 130

Query: 118 AELLARLKRLVPAHELVVVAGSLPRGIDSQWFVQLLNSLKALGVRVALDTSGAALRDGLA 177
             LL  +  L   +   V++GS+P G+    + +++ +L   G  V +D SG  LR  +A
Sbjct: 131 RGLLTVVDDLAVTNRTFVLSGSVPAGVPDTAYTEMVTALHRRGAFVVVDASGPPLRHAVA 190

Query: 178 TRPWLIKPNEEELAEARGIELSGSSALAAEAQRLQEEGIEHVVVSQGADGVSWFSPGAAL 237
            RP ++KPN  ELAE  G  L   + +   A+ L E GI  VVVS GA+G  +   G AL
Sbjct: 191 ARPDMVKPNAAELAELLGRPLKDRAEVVRAARELSESGIALVVVSLGAEGAVFVEGGRAL 250

Query: 238 HASPPKVRVVSTVGAGDSLLAGMLHGLLEGWPAERTLTHATAIAAQAVGQVGFGITDTAQ 297
            A PP V V STVGAGD+++AG++   LEG   E      TA AA  + ++G  +    +
Sbjct: 251 LAMPPPVEVASTVGAGDAMVAGVVAARLEGMGLEDCARRGTAFAAGTLSRLGPELPPPER 310

Query: 298 LAELQAAVRLQPL 310
           LAEL  AVR++ L
Sbjct: 311 LAELMRAVRVEEL 323


Lambda     K      H
   0.316    0.132    0.371 

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: 251
Number of extensions: 12
Number of successful extensions: 3
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: 312
Length of database: 323
Length adjustment: 27
Effective length of query: 285
Effective length of database: 296
Effective search space:    84360
Effective search space used:    84360
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 48 (23.1 bits)

Align candidate AZOBR_RS30840 AZOBR_RS30840 (hypothetical protein)
to HMM TIGR03828 (pfkB: 1-phosphofructokinase (EC 2.7.1.56))

# 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/TIGR03828.hmm
# target sequence database:        /tmp/gapView.10783.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03828  [M=305]
Accession:   TIGR03828
Description: pfkB: 1-phosphofructokinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    1.7e-96  308.9   0.2    1.9e-96  308.7   0.2    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS30840  AZOBR_RS30840 hypothetical prote


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS30840  AZOBR_RS30840 hypothetical protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  308.7   0.2   1.9e-96   1.9e-96       1     305 []      11     321 ..      11     321 .. 0.97

  Alignments for each domain:
  == domain 1  score: 308.7 bits;  conditional E-value: 1.9e-96
                                 TIGR03828   1 IlTvTlNpaiDktieleelelgevnrveserldagGKGinVarvLkklg.....vevvalgflGgftge 64 
                                               ++TvTlN+aiD+t+++ ++ +g+vnr+ +e   agGKGinVa +L+ +      ++v+a+gflG+++ +
  lcl|FitnessBrowser__azobra:AZOBR_RS30840  11 VVTVTLNAAIDQTLDVPGFAAGAVNRAVAETRTAGGKGINVAAFLAGASlaggaTPVTATGFLGEENTA 79 
                                               79******************************************9977522222689************ PP

                                 TIGR03828  65 eiealleeegiktdfvevkgetRinvkikes.sgeetklnepGpeiseeeleallekleeqlkegdvlv 132
                                                ++al++++gi +++++++g +R+n+k++++  + +t++n pG ++ +e +  ll+ +++ + +++++v
  lcl|FitnessBrowser__azobra:AZOBR_RS30840  80 VFDALFRRRGIRDRCLRLAGRSRVNIKLVDReGHSVTDINLPGLHVPAESWRGLLTVVDDLAVTNRTFV 148
                                               *******************************9999********************************** PP

                                 TIGR03828 133 laGSlPrgvpedlyaelikllrekgakvilDtsgeaLlkvlkakplliKPNkeEleellgrelkteeev 201
                                               l+GS+P+gvp+++y e++ +l+++ga v++D+sg++L+++++a+p+++KPN++El+ellgr lk+ +ev
  lcl|FitnessBrowser__azobra:AZOBR_RS30840 149 LSGSVPAGVPDTAYTEMVTALHRRGAFVVVDASGPPLRHAVAARPDMVKPNAAELAELLGRPLKDRAEV 217
                                               ********************************************************************* PP

                                 TIGR03828 202 ieaarkllekgvenvlislGadGallvtkegalfakapkievkstvGAGDsmvAgfllalekglsleea 270
                                               ++aar+l e+g++ v++slGa+Ga++v+  +al a +p +ev+stvGAGD+mvAg+++a  +g+ le++
  lcl|FitnessBrowser__azobra:AZOBR_RS30840 218 VRAARELSESGIALVVVSLGAEGAVFVEGGRALLAMPPPVEVASTVGAGDAMVAGVVAARLEGMGLEDC 286
                                               ********************************************************************* PP

                                 TIGR03828 271 lrlavAvgaaaassegtelpdledieelleevkie 305
                                                r ++A++a + s+ g elp +e+++el + v++e
  lcl|FitnessBrowser__azobra:AZOBR_RS30840 287 ARRGTAFAAGTLSRLGPELPPPERLAELMRAVRVE 321
                                               ********************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (305 nodes)
Target sequences:                          1  (323 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 10.85
//
[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:

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