GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuB in Leptospirillum ferrooxidans C2-3

Align 3-isopropylmalate dehydrogenase; 3-IPM-DH; Beta-IPM dehydrogenase; IMDH; EC 1.1.1.85 (characterized)
to candidate WP_014450629.1 LFE_RS12730 3-isopropylmalate dehydrogenase

Query= SwissProt::Q56268
         (358 letters)



>NCBI__GCF_000284315.1:WP_014450629.1
          Length = 367

 Score =  399 bits (1024), Expect = e-116
 Identities = 201/354 (56%), Positives = 264/354 (74%), Gaps = 5/354 (1%)

Query: 3   KIAIFAGDGIGPEIVAAARQVLDAVDQA-----AHLGLRCTEGLVGGAALDASDDPLPAA 57
           +I +  GDGIGPE+    R+++  ++++         +   EGL+GGAA DA+  PLP  
Sbjct: 8   QILLLPGDGIGPEVTVPVRELVSEINRSESGSQGKFQIELLEGLIGGAATDATGKPLPKE 67

Query: 58  SLQLAMAADAVILGAVGGPRWDAYPPAKRPEQGLLRLRKGLDLYANLRPAQIFPQLLDAS 117
           +L++A + DAV+L AVGGP++D  P   RPE+ LL +R+ L  +ANLRPA++FP+L+DAS
Sbjct: 68  TLEMADSCDAVLLAAVGGPKYDLLPYELRPERALLGIREHLGAFANLRPARLFPELVDAS 127

Query: 118 PLRPELVRDVDILVVRELTGDIYFGQPRGLEVIDGKRRGFNTMVYDEDEIRRIAHVAFRA 177
            L+PE++ D+D++VVRELTG IYFG+PRG+   +G RRG NT  Y E EI R+A VAF  
Sbjct: 128 TLKPEVISDLDLMVVRELTGGIYFGKPRGIVEENGIRRGINTETYTEPEIERVARVAFDL 187

Query: 178 AQGRRKQLCSVDKANVLETTRLWREVVTEVARDYPDVRLSHMYVDNAAMQLIRAPAQFDV 237
           A+ R  ++ SVDKANVLE++ LWREVV  V +DYPDV L HMYVDNAAMQL+R P QFDV
Sbjct: 188 ARKRSHRVTSVDKANVLESSVLWREVVIRVHKDYPDVTLDHMYVDNAAMQLVRKPKQFDV 247

Query: 238 LLTGNMFGDILSDEASQLTGSIGMLPSASLGEGRAMYEPIHGSAPDIAGQDKANPLATIL 297
           ++TGN+FGDILSDEASQLTGSIGML SAS+G    +YEPIHGSAPDIAG++ ANP+A IL
Sbjct: 248 IVTGNLFGDILSDEASQLTGSIGMLASASIGGKTGLYEPIHGSAPDIAGKNIANPMAMIL 307

Query: 298 SVAMMLRHSLNAEPWAQRVEAAVQRVLDQGLRTADIAAPGTPVIGTKAMGAAVV 351
           S+A++LR+SLN E  AQR+E +V  VL QG RTADIA     V+GT+ MG  ++
Sbjct: 308 SLALLLRYSLNREDLAQRIERSVSSVLAQGFRTADIAQVKGQVLGTREMGEKII 361


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: 381
Number of extensions: 9
Number of successful extensions: 2
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: 367
Length adjustment: 29
Effective length of query: 329
Effective length of database: 338
Effective search space:   111202
Effective search space used:   111202
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 WP_014450629.1 LFE_RS12730 (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.2702041.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-148  479.4   0.0   3.6e-148  479.2   0.0    1.0  1  NCBI__GCF_000284315.1:WP_014450629.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000284315.1:WP_014450629.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  479.2   0.0  3.6e-148  3.6e-148       2     349 .]       9     360 ..       8     360 .. 0.96

  Alignments for each domain:
  == domain 1  score: 479.2 bits;  conditional E-value: 3.6e-148
                             TIGR00169   2 iavLpGDgiGpevvaealkvLkavee.....rfelklefeealiGGaaidatgePlpeetlkackeadavLlg 69 
                                           i +LpGDgiGpev+    + + +++      + ++++e  e liGGaa datg+Plp+etl+ +++ davLl+
  NCBI__GCF_000284315.1:WP_014450629.1   9 ILLLPGDGIGPEVTVPVRELVSEINRsesgsQGKFQIELLEGLIGGAATDATGKPLPKETLEMADSCDAVLLA 81 
                                           899**********9999998888875312234467888889******************************** PP

                             TIGR00169  70 avGGpkWdnlprdvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGiYfGep 142
                                           avGGpk+d lp + rPe++LL +r++l+ fanLrPa+lf++L+++s+lk+e+++++Dl+vvreLtgGiYfG+p
  NCBI__GCF_000284315.1:WP_014450629.1  82 AVGGPKYDLLPYELRPERALLGIREHLGAFANLRPARLFPELVDASTLKPEVISDLDLMVVRELTGGIYFGKP 154
                                           ************************************************************************* PP

                             TIGR00169 143 kereeaeeekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiakeyPdvele 215
                                           +++ e++  +++++te+Yt++eier+arvaf larkr ++vtsvDkanvLess lWr++v  ++k+yPdv+l+
  NCBI__GCF_000284315.1:WP_014450629.1 155 RGIVEENGIRRGINTETYTEPEIERVARVAFDLARKRSHRVTSVDKANVLESSVLWREVVIRVHKDYPDVTLD 227
                                           *****888***************************************************************** PP

                             TIGR00169 216 hlyiDnaamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslsskglalfepvhgsapdiagkgi 288
                                           h+y+DnaamqLv++P+q+dv+vt+nlfGDilsDeas +tGs+G+L sas++  +++l+ep+hgsapdiagk+i
  NCBI__GCF_000284315.1:WP_014450629.1 228 HMYVDNAAMQLVRKPKQFDVIVTGNLFGDILSDEASQLTGSIGMLASASIG-GKTGLYEPIHGSAPDIAGKNI 299
                                           ***************************************************.6789***************** PP

                             TIGR00169 289 anpiaailsaalllryslnleeaaeaieaavkkvleegkrtedlaseattavstkeveeel 349
                                           anp+a+ils+alllrysln e+ a++ie++v+ vl++g rt+d+a+ +++  +t+e++e++
  NCBI__GCF_000284315.1:WP_014450629.1 300 ANPMAMILSLALLLRYSLNREDLAQRIERSVSSVLAQGFRTADIAQVKGQVLGTREMGEKI 360
                                           *********************************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (367 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: 26.18
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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