Alignments for a candidate for leuB in Herbaspirillum seropedicae SmR1

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuB in Herbaspirillum seropedicae SmR1

Align 3-isopropylmalate dehydrogenase; 3-IPM-DH; Beta-IPM dehydrogenase; IMDH; EC 1.1.1.85 (characterized)
to candidate HSERO_RS16500 HSERO_RS16500 3-isopropylmalate dehydrogenase

Query= SwissProt::Q56268
         (358 letters)



>FitnessBrowser__HerbieS:HSERO_RS16500
          Length = 356

 Score =  403 bits (1036), Expect = e-117
 Identities = 218/358 (60%), Positives = 261/358 (72%), Gaps = 10/358 (2%)

Query: 3   KIAIFAGDGIGPEIVAAARQVLDAVDQAAHLGLRCTEGLVGGAALDASDDPLPAASLQLA 62
           KIAI  GDGIGPEIV  A +VL+A+D+   +        VGGA  +A   PLP  +L+LA
Sbjct: 2   KIAILPGDGIGPEIVNEAVRVLNALDEKFEM----ETAPVGGAGYEAHGHPLPDGTLKLA 57

Query: 63  MAADAVILGAVGGPRWDAYPPAKRPEQGLLRLRKGLDLYANLRPAQIFPQLLDASPLRPE 122
             ADA++ GAVG  ++D    A RPEQ +L LRK L L+AN RPA  +P+L  AS L+PE
Sbjct: 58  KEADAILFGAVGDWKYDKLERALRPEQAILGLRKHLQLFANFRPAICYPELTGASSLKPE 117

Query: 123 LVRDVDILVVRELTGDIYFGQPRGLEV-----IDGKRRGFNTMVYDEDEIRRIAHVAFRA 177
           LV ++DIL+VREL GDIYFGQPRG+         G R GF+TM Y E EIRRIAHVAF+A
Sbjct: 118 LVANLDILIVRELNGDIYFGQPRGMREAPDGPFKGAREGFDTMRYSEPEIRRIAHVAFQA 177

Query: 178 AQGRRKQLCSVDKANVLETTRLWREVVTEVARDYPDVRLSHMYVDNAAMQLIRAPAQFDV 237
           A  R K+LCSVDKANVLET + W+++VTEV ++YPDV LSHMYVDNAAMQL++AP  FDV
Sbjct: 178 AAKRGKRLCSVDKANVLETFQFWKDIVTEVGKEYPDVELSHMYVDNAAMQLVKAPKNFDV 237

Query: 238 LLTGNMFGDILSDEASQLTGSIGMLPSASL-GEGRAMYEPIHGSAPDIAGQDKANPLATI 296
           ++TGNMFGDILSD A+ LTGSIGMLPSASL    + +YEP HGSAPDIAG+  ANPLATI
Sbjct: 238 IVTGNMFGDILSDAAAMLTGSIGMLPSASLDANNKGLYEPSHGSAPDIAGRGIANPLATI 297

Query: 297 LSVAMMLRHSLNAEPWAQRVEAAVQRVLDQGLRTADIAAPGTPVIGTKAMGAAVVNAL 354
           LS AMMLR SLN    A R+E AV++VL QGLRTADI   G   + T+ MG AVV AL
Sbjct: 298 LSAAMMLRFSLNKAEQADRIENAVKKVLAQGLRTADIYEEGCTKVNTQQMGEAVVKAL 355


Lambda     K      H
   0.320    0.137    0.396 

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: 407
Number of extensions: 16
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: 358
Length of database: 356
Length adjustment: 29
Effective length of query: 329
Effective length of database: 327
Effective search space:   107583
Effective search space used:   107583
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: 49 (23.5 bits)

Align candidate HSERO_RS16500 HSERO_RS16500 (3-isopropylmalate dehydrogenase)
to HMM TIGR00169 (leuB: 3-isopropylmalate dehydrogenase (EC 1.1.1.85))

# 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.aa/TIGR00169.hmm
# target sequence database:        /tmp/gapView.23261.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00169  [M=349]
Accession:   TIGR00169
Description: leuB: 3-isopropylmalate dehydrogenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   3.4e-150  485.8   0.0   3.9e-150  485.7   0.0    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS16500  HSERO_RS16500 3-isopropylmalate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS16500  HSERO_RS16500 3-isopropylmalate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  485.7   0.0  3.9e-150  3.9e-150       1     348 [.       2     350 ..       2     351 .. 0.97

  Alignments for each domain:
  == domain 1  score: 485.7 bits;  conditional E-value: 3.9e-150
                                  TIGR00169   1 kiavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLl 68 
                                                kia+LpGDgiGpe+v+ea++vL+a++e+    +e+e+a +GGa  +a+g+Plp+ tlk +keada+L+
  lcl|FitnessBrowser__HerbieS:HSERO_RS16500   2 KIAILPGDGIGPEIVNEAVRVLNALDEK----FEMETAPVGGAGYEAHGHPLPDGTLKLAKEADAILF 65 
                                                79***********************996....567899****************************** PP

                                  TIGR00169  69 gavGGpkWdnlprdvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgG 136
                                                gavG  k+d+l r  rPe+++L lrk+l+lfan+rPa  +++L+ +s+lk+e+v ++D+++vreL g 
  lcl|FitnessBrowser__HerbieS:HSERO_RS16500  66 GAVGDWKYDKLERALRPEQAILGLRKHLQLFANFRPAICYPELTGASSLKPELVANLDILIVRELNGD 133
                                                ******************************************************************** PP

                                  TIGR00169 137 iYfGepkereeaee.....ekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWr 199
                                                iYfG+p++++ea +      ++++dt++Y+++ei+ria+vaf++a+kr k+++svDkanvLe+ ++W+
  lcl|FitnessBrowser__HerbieS:HSERO_RS16500 134 IYFGQPRGMREAPDgpfkgAREGFDTMRYSEPEIRRIAHVAFQAAAKRGKRLCSVDKANVLETFQFWK 201
                                                ********99974322324789********************************************** PP

                                  TIGR00169 200 ktveeiakeyPdvelehlyiDnaamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslss 267
                                                ++v+e+ keyPdvel+h+y+DnaamqLvk+P+++dv+vt+n+fGDilsD a+++tGs+G+LPsasl  
  lcl|FitnessBrowser__HerbieS:HSERO_RS16500 202 DIVTEVGKEYPDVELSHMYVDNAAMQLVKAPKNFDVIVTGNMFGDILSDAAAMLTGSIGMLPSASLDA 269
                                                ******************************************************************** PP

                                  TIGR00169 268 kglalfepvhgsapdiagkgianpiaailsaalllryslnleeaaeaieaavkkvleegkrtedlase 335
                                                + ++l+ep hgsapdiag+gianp+a+ilsaa++lr sln+ e+a++ie+avkkvl++g rt+d+++e
  lcl|FitnessBrowser__HerbieS:HSERO_RS16500 270 NNKGLYEPSHGSAPDIAGRGIANPLATILSAAMMLRFSLNKAEQADRIENAVKKVLAQGLRTADIYEE 337
                                                ******************************************************************** PP

                                  TIGR00169 336 attavstkeveee 348
                                                ++t+v t++++e 
  lcl|FitnessBrowser__HerbieS:HSERO_RS16500 338 GCTKVNTQQMGEA 350
                                                **********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (356 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.23
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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
changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis