Alignments for a candidate for tpi in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for tpi in Herbaspirillum seropedicae SmR1

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate HSERO_RS08805 HSERO_RS08805 triosephosphate isomerase

Query= BRENDA::P0A858
         (255 letters)



>FitnessBrowser__HerbieS:HSERO_RS08805
          Length = 238

 Score =  210 bits (535), Expect = 2e-59
 Identities = 111/238 (46%), Positives = 147/238 (61%), Gaps = 1/238 (0%)

Query: 12  LNGSRHMVHELVSNLRKELAGVAGCAVAIAPPEMYIDMAKREAEGSHIMLGAQNVDLNLS 71
           +NGS      LV+ +++ LA  A C VA+  P  Y+   +    GS + LGAQ++  + S
Sbjct: 1   MNGSLAANAALVAGIKEGLAAQA-CDVAVCVPAPYLAQVQALVAGSPVGLGAQDMSAHAS 59

Query: 72  GAFTGETSAAMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQGLTPVLCIGETE 131
           GA+TGE SA+ML++ G QY+I+GHSERR YH ESD  +A K     + GL P++C+GET 
Sbjct: 60  GAYTGEVSASMLQEFGVQYVILGHSERRAYHGESDAAVAAKTVAALKAGLVPLVCVGETL 119

Query: 132 AENEAGKTEEVCARQIDAVLKTQGAAAFEGAVIAYEPVWAIGTGKSATPAQAQAVHKFIR 191
            + EAG+T  V   Q+D VL    A      V+AYEPVWAIGTGK+ATP  AQ VH  +R
Sbjct: 120 EQREAGQTNAVVGGQLDVVLAALSAEEAARIVVAYEPVWAIGTGKTATPEMAQEVHAMLR 179

Query: 192 DHIAKVDANIAEQVIIQYGGSVNASNAAELFAQPDIDGALVGGASLKADAFAVIVKAA 249
             +    A  A +V I YGGS+   NA +L A  DIDG L+GGA+LKA  F  I+ AA
Sbjct: 180 ARLGAKSAEAAAKVCILYGGSMKPDNAQQLLAMGDIDGGLIGGAALKAADFLAIINAA 237


Lambda     K      H
   0.316    0.130    0.366 

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: 184
Number of extensions: 6
Number of successful extensions: 1
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: 255
Length of database: 238
Length adjustment: 24
Effective length of query: 231
Effective length of database: 214
Effective search space:    49434
Effective search space used:    49434
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: 46 (22.3 bits)

Align candidate HSERO_RS08805 HSERO_RS08805 (triosephosphate isomerase)
to HMM TIGR00419 (tpiA: triose-phosphate isomerase (EC 5.3.1.1))

# 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/TIGR00419.hmm
# target sequence database:        /tmp/gapView.9344.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00419  [M=228]
Accession:   TIGR00419
Description: tim: triose-phosphate isomerase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
    4.6e-58  182.7   8.6    5.3e-58  182.5   8.6    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS08805  HSERO_RS08805 triosephosphate is


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS08805  HSERO_RS08805 triosephosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  182.5   8.6   5.3e-58   5.3e-58       9     227 ..       2     227 ..       1     228 [. 0.94

  Alignments for each domain:
  == domain 1  score: 182.5 bits;  conditional E-value: 5.3e-58
                                  TIGR00419   9 nesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnvdavksGaftGeisA 75 
                                                n+s+   + +va ++e +a +  + vav +p  +l  v+  v  s + ++Aq++ a+ sGa+tGe+sA
  lcl|FitnessBrowser__HerbieS:HSERO_RS08805   2 NGSLAANAALVAGIKEGLAAQ-ACDVAVCVPAPYLAQVQALVAgSPVGLGAQDMSAHASGAYTGEVSA 68 
                                                8999999**********9976.58999999999********99999********************** PP

                                  TIGR00419  76 emlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleere.......aartin 136
                                                 ml+++G+++v++gHsErR+++ e+d  +++k   + + gl ++vCvgetle+re       ++ +++
  lcl|FitnessBrowser__HerbieS:HSERO_RS08805  69 SMLQEFGVQYVILGHSERRAYHGESDAAVAAKTVAALKAGLVPLVCVGETLEQREagqtnavVGGQLD 136
                                                ********************************999999*****************7776666667777 PP

                                  TIGR00419 137 nvattaaaaAlepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaa 204
                                                +v+   +a      vvA+EPv++iGtGk++++  a++v++++r  l   s+e a +v +lyG+s++  
  lcl|FitnessBrowser__HerbieS:HSERO_RS08805 137 VVLAALSAEEAARIVVAYEPVWAIGTGKTATPEMAQEVHAMLRARLGAKSAEAAAKVCILYGGSMKPD 204
                                                77777777778999****************************************************** PP

                                  TIGR00419 205 edaelaaqldvdGvLlasavlka 227
                                                ++++l a  d+dG L+++a lka
  lcl|FitnessBrowser__HerbieS:HSERO_RS08805 205 NAQQLLAMGDIDGGLIGGAALKA 227
                                                **********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (228 nodes)
Target sequences:                          1  (238 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: 00:00:00.01
# Mc/sec: 5.29
//
[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