Aligments for a candidate for 1pfk in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Aligments 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.15599.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 6.81
//
[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