GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuB in Pedobacter sp. GW460-11-11-14-LB5

Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate CA265_RS15850 CA265_RS15850 3-isopropylmalate dehydrogenase

Query= BRENDA::Q9SA14
         (404 letters)



>FitnessBrowser__Pedo557:CA265_RS15850
          Length = 363

 Score =  353 bits (906), Expect = e-102
 Identities = 184/362 (50%), Positives = 253/362 (69%), Gaps = 9/362 (2%)

Query: 45  NITLLPGDGIGPEVISVAKNVLQKAGFLQGLEFDFQEMPFGGAALDLVGVPLPEETSTAA 104
           NI ++PGDGIGPEV +  K  L+K   + G EF F+E   G AA+++ G PLP+ET   A
Sbjct: 4   NILVIPGDGIGPEVTTWGKAALEKIAEIFGHEFAFEEALMGHAAIEVTGEPLPDETLEKA 63

Query: 105 KQSDAILLGAIGGYKWDKNEK-HLRPEMGLLNIRRDLNVFANLRPATVLPQLVDASTLKK 163
           +QSDAIL GAIG  K+D +    +RPE GLL IR++L +FANLRP  +  +L+ AS++K 
Sbjct: 64  RQSDAILFGAIGHAKYDNDPSLKVRPEQGLLKIRKELGLFANLRPILLFDELLQASSIKP 123

Query: 164 EVAQGVDMMIVRELTGGIYFGEPRGITINENGEEVGFNTEIYAAHEIDRIARVAFETARK 223
           E+ +G D++  RELTG +YFGE               +  IY  +E++RIA  A++ A++
Sbjct: 124 EILRGTDILFFRELTGDVYFGEKT----RSEDRNTASDLMIYHRYEVERIAHKAYQAAQQ 179

Query: 224 RRGKLCSVDKANVLDASILWRKRVTALASEYPDVELSHMYVDNAAMQLVRDPKQFDTIVT 283
           R  +LCSVDKANVL++S LWR+ V  +A +YPDVE  HM++DNAAMQL+++PK+FD ++T
Sbjct: 180 RNKRLCSVDKANVLESSRLWRETVQEIAKQYPDVETEHMFIDNAAMQLIKNPKKFDVVLT 239

Query: 284 NNIFGDILSDEASMITGSIGMLPSASLGESGPGLFEPIHGSAPDIAGQDKANPLATILSA 343
            N+FGDIL+DEAS I GS+GML SAS+GES  G FEPIHGSA DIAG+D ANPLA+ILSA
Sbjct: 240 ANLFGDILTDEASQIAGSMGMLASASVGES-TGFFEPIHGSAHDIAGKDLANPLASILSA 298

Query: 344 AMLLKYGLGEEKAAKMIEDAVVDALNKGFRTGDIYSPGN---KLVGCKEMGEEVLKSVDS 400
           A++L+ G G ++ AK++ D +   L +GFRT DI        K++G  EMG+ VLK +  
Sbjct: 299 ALMLEIGFGLKEEAKLLVDTIDQVLKEGFRTHDIADQSTNRFKVLGTAEMGKLVLKFLSQ 358

Query: 401 KV 402
           K+
Sbjct: 359 KL 360


Lambda     K      H
   0.317    0.136    0.389 

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: 394
Number of extensions: 14
Number of successful extensions: 5
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: 404
Length of database: 363
Length adjustment: 30
Effective length of query: 374
Effective length of database: 333
Effective search space:   124542
Effective search space used:   124542
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate CA265_RS15850 CA265_RS15850 (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.28275.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   3.1e-140  453.1   0.0   3.5e-140  452.9   0.0    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS15850  CA265_RS15850 3-isopropylmalate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS15850  CA265_RS15850 3-isopropylmalate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  452.9   0.0  3.5e-140  3.5e-140       1     339 [.       4     339 ..       4     352 .. 0.97

  Alignments for each domain:
  == domain 1  score: 452.9 bits;  conditional E-value: 3.5e-140
                                  TIGR00169   1 kiavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLl 68 
                                                +i v+pGDgiGpev++   + L++++e f++++ feeal+G aai+ tgePlp+etl++++++da+L+
  lcl|FitnessBrowser__Pedo557:CA265_RS15850   4 NILVIPGDGIGPEVTTWGKAALEKIAEIFGHEFAFEEALMGHAAIEVTGEPLPDETLEKARQSDAILF 71 
                                                689***************************************************************** PP

                                  TIGR00169  69 gavGGpkWdnlpr.dvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtg 135
                                                ga+G  k+dn p+ +vrPe+gLLk+rkel+lfanLrP+ lf++L+++s++k+ei +g+D++  reLtg
  lcl|FitnessBrowser__Pedo557:CA265_RS15850  72 GAIGHAKYDNDPSlKVRPEQGLLKIRKELGLFANLRPILLFDELLQASSIKPEILRGTDILFFRELTG 139
                                                **********997589**************************************************** PP

                                  TIGR00169 136 GiYfGepkereeaeeekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktve 203
                                                 +YfGe++ +e+   +++a d + Y+++e+eria++a+++a++r+k+++svDkanvLessrlWr+tv+
  lcl|FitnessBrowser__Pedo557:CA265_RS15850 140 DVYFGEKTRSED---RNTASDLMIYHRYEVERIAHKAYQAAQQRNKRLCSVDKANVLESSRLWRETVQ 204
                                                ******998888...899************************************************** PP

                                  TIGR00169 204 eiakeyPdvelehlyiDnaamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslsskgla 271
                                                eiak+yPdve eh++iDnaamqL+k+P+++dvv+t nlfGDil Deas i+Gs+G+L sas++ + ++
  lcl|FitnessBrowser__Pedo557:CA265_RS15850 205 EIAKQYPDVETEHMFIDNAAMQLIKNPKKFDVVLTANLFGDILTDEASQIAGSMGMLASASVG-ESTG 271
                                                ***************************************************************.8899 PP

                                  TIGR00169 272 lfepvhgsapdiagkgianpiaailsaalllryslnleeaaeaieaavkkvleegkrtedlaseatta 339
                                                +fep+hgsa diagk++anp+a ilsaal+l+ +++l+e+a+ + +++++vl+eg rt+d+a+++t++
  lcl|FitnessBrowser__Pedo557:CA265_RS15850 272 FFEPIHGSAHDIAGKDLANPLASILSAALMLEIGFGLKEEAKLLVDTIDQVLKEGFRTHDIADQSTNR 339
                                                ***************************************************************99764 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (363 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: 8.63
//
[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:

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