Alignments for a candidate for argG in Klebsiella michiganensis M5al

GapMind for Amino acid biosynthesis

Alignments for a candidate for argG in Klebsiella michiganensis M5al

Align argininosuccinate synthase (characterized)
to candidate BWI76_RS25115 BWI76_RS25115 argininosuccinate synthase

Query= CharProtDB::CH_024687
         (447 letters)



>FitnessBrowser__Koxy:BWI76_RS25115
          Length = 447

 Score =  855 bits (2210), Expect = 0.0
 Identities = 419/447 (93%), Positives = 440/447 (98%)

Query: 1   MTTILKHLPVGQRIGIAFSGGLDTSAALLWMRQKGAVPYAYTANLGQPDEEDYDAIPRRA 60
           MTTILKHLPVGQRIGIAFSGGLDTSAALLWMR+KGAVPYAYTANLGQPDE+DYDAIPRRA
Sbjct: 1   MTTILKHLPVGQRIGIAFSGGLDTSAALLWMRKKGAVPYAYTANLGQPDEDDYDAIPRRA 60

Query: 61  MEYGAENARLIDCRKQLVAEGIAAIQCGAFHNTTGGLTYFNTTPLGRAVTGTMLVAAMKE 120
            EYGAE ARLIDCRKQLVAEGIAAIQCGAFHNTTGGLTYFNTTPLGRAVTGTMLVAAMKE
Sbjct: 61  KEYGAEGARLIDCRKQLVAEGIAAIQCGAFHNTTGGLTYFNTTPLGRAVTGTMLVAAMKE 120

Query: 121 DGVNIWGDGSTYKGNDIERFYRYGLLTNAELQIYKPWLDTDFIDELGGRHEMSEFMIACG 180
           DGVNIWGDGSTYKGNDIERFYRYGLLTNAEL+IYKPWLD+DFIDELGGR EMSEFMI+CG
Sbjct: 121 DGVNIWGDGSTYKGNDIERFYRYGLLTNAELKIYKPWLDSDFIDELGGRQEMSEFMISCG 180

Query: 181 FDYKMSVEKAYSTDSNMLGATHEAKDLEYLNSSVKIVNPIMGVKFWDESVKIPAEEVTVR 240
           FDYKMSVEKAYSTDSNMLGATHEAKDLE+LNSSVKIVNPIMGVKFWDESVKIPAEEVTVR
Sbjct: 181 FDYKMSVEKAYSTDSNMLGATHEAKDLEFLNSSVKIVNPIMGVKFWDESVKIPAEEVTVR 240

Query: 241 FEQGHPVALNGKTFSDDVEMMLEANRIGGRHGLGMSDQIENRIIEAKSRGIYEAPGMALL 300
           FEQGHPVALNG+TFSDDVE+MLEANRIGGRHGLGMSDQIENRIIEAKSRGIYEAPGMALL
Sbjct: 241 FEQGHPVALNGQTFSDDVELMLEANRIGGRHGLGMSDQIENRIIEAKSRGIYEAPGMALL 300

Query: 301 HIAYERLLTGIHNEDTIEQYHAHGRQLGRLLYQGRWFDSQALMLRDSLQRWVASQITGEV 360
           HIAYERLLTGIHNEDTIEQYHAHGRQLGRLLYQGRWFDSQALMLRD LQRWVASQITGEV
Sbjct: 301 HIAYERLLTGIHNEDTIEQYHAHGRQLGRLLYQGRWFDSQALMLRDGLQRWVASQITGEV 360

Query: 361 TLELRRGNDYSILNTVSENLTYKPERLTMEKGDSVFSPDDRIGQLTMRNLDITDTREKLF 420
           TLELRRGNDYSILNTVS+NLTYK ERLTMEKGDS+FS +DRIGQLTMRNLDITDTR+KLF
Sbjct: 361 TLELRRGNDYSILNTVSDNLTYKAERLTMEKGDSMFSAEDRIGQLTMRNLDITDTRDKLF 420

Query: 421 GYAKTGLLSSSAASGVPQVENLENKGQ 447
           GYA++GLL++S+A+G+PQVENLE+K +
Sbjct: 421 GYAQSGLLTASSATGLPQVENLESKSK 447


Lambda     K      H
   0.317    0.135    0.397 

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: 778
Number of extensions: 14
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: 447
Length of database: 447
Length adjustment: 33
Effective length of query: 414
Effective length of database: 414
Effective search space:   171396
Effective search space used:   171396
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: 51 (24.3 bits)

Align candidate BWI76_RS25115 BWI76_RS25115 (argininosuccinate synthase)
to HMM TIGR00032 (argG: argininosuccinate synthase (EC 6.3.4.5))

# 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/TIGR00032.hmm
# target sequence database:        /tmp/gapView.25909.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00032  [M=394]
Accession:   TIGR00032
Description: argG: argininosuccinate synthase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   3.9e-170  552.3   0.0   4.4e-170  552.1   0.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS25115  BWI76_RS25115 argininosuccinate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS25115  BWI76_RS25115 argininosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  552.1   0.0  4.4e-170  4.4e-170       1     393 [.      13     419 ..      13     420 .. 0.99

  Alignments for each domain:
  == domain 1  score: 552.1 bits;  conditional E-value: 4.4e-170
                               TIGR00032   1 kvvlaysGGlDtsvalklleekgaeviavtvdvGqp.eedldaieekalklGaekayviDareefvkdylf 70 
                                             ++++a+sGGlDts+al+++++kga+++a+t+++Gqp e+d+dai+++a+++Gae a++iD+r+++v++ ++
  lcl|FitnessBrowser__Koxy:BWI76_RS25115  13 RIGIAFSGGLDTSAALLWMRKKGAVPYAYTANLGQPdEDDYDAIPRRAKEYGAEGARLIDCRKQLVAE-GI 82 
                                             689*****************************************************************.** PP

                               TIGR00032  71 aaiqanavyegk....YllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFelsilllnpdlkv 137
                                             aaiq++a+++++    Y+++t+L+R++++++lv+++k++g++++++G+t+KGnD++RF++++ll+n++lk+
  lcl|FitnessBrowser__Koxy:BWI76_RS25115  83 AAIQCGAFHNTTggltYFNTTPLGRAVTGTMLVAAMKEDGVNIWGDGSTYKGNDIERFYRYGLLTNAELKI 153
                                             ***********99999******************************************************* PP

                               TIGR00032 138 iaPvreleli.....ReeeieyaaekGievpvekekaysiDenllgrsiEageLEdp.steppediyelvk 202
                                             ++P+++ ++i     R+e++e+++++G+++++++ekays+D+n+lg+++Ea++LE + s++++++++++vk
  lcl|FitnessBrowser__Koxy:BWI76_RS25115 154 YKPWLDSDFIdelggRQEMSEFMISCGFDYKMSVEKAYSTDSNMLGATHEAKDLEFLnSSVKIVNPIMGVK 224
                                             *********************************************************999*********** PP

                               TIGR00032 203 dpiektedepevveieFekGvPvalngesle.pvelilkaneiagkhGvGriDivEdRiiglKsReiYEap 272
                                             +++e++++ +e+v+++Fe+G+Pvalng++++ +vel+l+an+i+g+hG+G++D++E+Rii++KsR+iYEap
  lcl|FitnessBrowser__Koxy:BWI76_RS25115 225 FWDESVKIPAEEVTVRFEQGHPVALNGQTFSdDVELMLEANRIGGRHGLGMSDQIENRIIEAKSRGIYEAP 295
                                             *******************************9*************************************** PP

                               TIGR00032 273 alllLikAhkdLetlvltkdvlefkeiveekyseliYkGlwfdplaeal.dalikktqervtGtvrvklfk 342
                                             +++lL++A+++L t+++++d++e+++++++++++l+Y+G+wfd++a +l d l++++++++tG+v+++l++
  lcl|FitnessBrowser__Koxy:BWI76_RS25115 296 GMALLHIAYERLLTGIHNEDTIEQYHAHGRQLGRLLYQGRWFDSQALMLrDGLQRWVASQITGEVTLELRR 366
                                             *************************************************99******************** PP

                               TIGR00032 343 Gnaivigrk.seyslYdeelvsfek.dkefdqkdaiGfikirglqikvyrekl 393
                                             Gn+++i+++ s++++Y++e++++ek d+ f+ +d+iG++++r+l+i+++r kl
  lcl|FitnessBrowser__Koxy:BWI76_RS25115 367 GNDYSILNTvSDNLTYKAERLTMEKgDSMFSAEDRIGQLTMRNLDITDTRDKL 419
                                             *************************99*********************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (394 nodes)
Target sequences:                          1  (447 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: 00:00:00.02
# Mc/sec: 8.19
//
[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