Alignments for a candidate for argH in Klebsiella michiganensis M5al

GapMind for Amino acid biosynthesis

Alignments for a candidate for argH in Klebsiella michiganensis M5al

Align argininosuccinate lyase (EC 4.3.2.1) (characterized)
to candidate BWI76_RS00855 BWI76_RS00855 argininosuccinate lyase

Query= ecocyc::ARGSUCCINLYA-MONOMER
         (457 letters)



>FitnessBrowser__Koxy:BWI76_RS00855
          Length = 457

 Score =  868 bits (2242), Expect = 0.0
 Identities = 438/456 (96%), Positives = 448/456 (98%)

Query: 1   MALWGGRFTQAADQRFKQFNDSLRFDYRLAEQDIVGSVAWSKALVTVGVLTAEEQAQLEE 60
           MALWGGRFTQAADQRFKQFNDSLRFDYRLAEQDIVGSVAWSKALVTVGVLTA+EQ QLEE
Sbjct: 1   MALWGGRFTQAADQRFKQFNDSLRFDYRLAEQDIVGSVAWSKALVTVGVLTADEQQQLEE 60

Query: 61  ALNVLLEDVRARPQQILESDAEDIHSWVEGKLIDKVGQLGKKLHTGRSRNDQVATDLKLW 120
           ALN+LLEDVRA PQQILESDAEDIHSWVEGKLIDKVGQLGKKLHTGRSRNDQVATDLKLW
Sbjct: 61  ALNILLEDVRANPQQILESDAEDIHSWVEGKLIDKVGQLGKKLHTGRSRNDQVATDLKLW 120

Query: 121 CKDTVSELLTANRQLQSALVETAQNNQDAVMPGYTHLQRAQPVTFAHWCLAYVEMLARDE 180
           CKDTV ELL+ANRQLQSALVETA+NNQDAVMPGYTHLQRAQPVTFAHWCLAYVEMLARDE
Sbjct: 121 CKDTVVELLSANRQLQSALVETAENNQDAVMPGYTHLQRAQPVTFAHWCLAYVEMLARDE 180

Query: 181 SRLQDALKRLDVSPLGCGALAGTAYEIDREQLAGWLGFASATRNSLDSVSDRDHVLELLS 240
           SRLQDALKRLDVSPLGCGALAGTAYEIDREQLAGWLGFASATRNSLDSVSDRDHVLELLS
Sbjct: 181 SRLQDALKRLDVSPLGCGALAGTAYEIDREQLAGWLGFASATRNSLDSVSDRDHVLELLS 240

Query: 241 AAAIGMVHLSRFAEDLIFFNTGEAGFVELSDRVTSGSSLMPQKKNPDALELIRGKCGRVQ 300
            A+IGMVHLSRFAEDLIFFNTGEAGFVELSDRVTSGSSLMPQKKNPDALELIRGKCGRVQ
Sbjct: 241 DASIGMVHLSRFAEDLIFFNTGEAGFVELSDRVTSGSSLMPQKKNPDALELIRGKCGRVQ 300

Query: 301 GALTGMMMTLKGLPLAYNKDMQEDKEGLFDALDTWLDCLHMAALVLDGIQVKRPRCQEAA 360
           GALTGMMMTLKGLPLAYNKDMQEDKEGLFDALDTWLDCLHMAALVLDGIQVKRPRC+EAA
Sbjct: 301 GALTGMMMTLKGLPLAYNKDMQEDKEGLFDALDTWLDCLHMAALVLDGIQVKRPRCEEAA 360

Query: 361 QQGYANATELADYLVAKGVPFREAHHIVGEAVVEAIRQGKPLEDLPLSELQKFSQVIDED 420
           QQGYANATELADYLVAKGVPFREAHHIVGEAVVEAI QGKPLEDLPL++LQKFS+VI ED
Sbjct: 361 QQGYANATELADYLVAKGVPFREAHHIVGEAVVEAIAQGKPLEDLPLADLQKFSRVIAED 420

Query: 421 VYPILSLQSCLDKRAAKGGVSPQQVAQAIAFAQARL 456
           VYPILSLQSCLDKRAAKGGVSPQQVAQAIA A+ RL
Sbjct: 421 VYPILSLQSCLDKRAAKGGVSPQQVAQAIADAKQRL 456


Lambda     K      H
   0.318    0.133    0.386 

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: 775
Number of extensions: 19
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: 457
Length of database: 457
Length adjustment: 33
Effective length of query: 424
Effective length of database: 424
Effective search space:   179776
Effective search space used:   179776
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 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate BWI76_RS00855 BWI76_RS00855 (argininosuccinate lyase)
to HMM TIGR00838 (argH: argininosuccinate lyase (EC 4.3.2.1))

# 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.aa/TIGR00838.hmm
# target sequence database:        /tmp/gapView.27091.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00838  [M=455]
Accession:   TIGR00838
Description: argH: argininosuccinate lyase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   3.5e-218  711.0   0.0     4e-218  710.9   0.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS00855  BWI76_RS00855 argininosuccinate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS00855  BWI76_RS00855 argininosuccinate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  710.9   0.0    4e-218    4e-218       1     454 [.       3     456 ..       3     457 .] 1.00

  Alignments for each domain:
  == domain 1  score: 710.9 bits;  conditional E-value: 4e-218
                               TIGR00838   1 lwggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevkeg. 70 
                                             lwggR+++++d+++++fn+sl+fD++lae+Di gs+a++kaL+++g+lt++e+++l+eaL+ l e+v+++ 
  lcl|FitnessBrowser__Koxy:BWI76_RS00855   3 LWGGRFTQAADQRFKQFNDSLRFDYRLAEQDIVGSVAWSKALVTVGVLTADEQQQLEEALNILLEDVRANp 73 
                                             7********************************************************************98 PP

                               TIGR00838  71 klelevdaeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalvekA 141
                                             ++ le+daeDiH++vE +lidkvg ++gkklhtgrsRnDqvatdl+l+++d+v el++a ++l++alve+A
  lcl|FitnessBrowser__Koxy:BWI76_RS00855  74 QQILESDAEDIHSWVEGKLIDKVG-QLGKKLHTGRSRNDQVATDLKLWCKDTVVELLSANRQLQSALVETA 143
                                             9999********************.********************************************** PP

                               TIGR00838 142 ekevetlmpgytHLqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidrellae 212
                                             e++++++mpgytHLqrAqP+t+aH++lay+eml+rD +Rl+dalkR+++sPlG+gAlagt++eidre+la 
  lcl|FitnessBrowser__Koxy:BWI76_RS00855 144 ENNQDAVMPGYTHLQRAQPVTFAHWCLAYVEMLARDESRLQDALKRLDVSPLGCGALAGTAYEIDREQLAG 214
                                             *********************************************************************** PP

                               TIGR00838 213 lLgFdavvensldavsdRDfiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgssimPqKKn 283
                                             +LgF+++++nsld+vsdRD+++Ells+a++ mvhlsr+aE+li+f++ E+gfvelsd+v+sgss+mPqKKn
  lcl|FitnessBrowser__Koxy:BWI76_RS00855 215 WLGFASATRNSLDSVSDRDHVLELLSDASIGMVHLSRFAEDLIFFNTGEAGFVELSDRVTSGSSLMPQKKN 285
                                             *********************************************************************** PP

                               TIGR00838 284 pDvaEliRgktgrviGnltglltilKalPlaYnkDlqEdkealfdalktveellevvtgllkelkvnkerl 354
                                             pD++EliRgk+grv+G ltg++++lK+lPlaYnkD+qEdke+lfdal+t+ ++l++++++l+ ++v++ r+
  lcl|FitnessBrowser__Koxy:BWI76_RS00855 286 PDALELIRGKCGRVQGALTGMMMTLKGLPLAYNKDMQEDKEGLFDALDTWLDCLHMAALVLDGIQVKRPRC 356
                                             *********************************************************************** PP

                               TIGR00838 355 eeaakknfalatdlAdylvrkGvPFReaheivGevvakaiekGkkleeltleelqklsekleedvlevldl 425
                                             eeaa++++a+at+lAdylv+kGvPFReah+ivGe+v++ai++Gk le+l+l+ lqk+s  + edv+ +l+l
  lcl|FitnessBrowser__Koxy:BWI76_RS00855 357 EEAAQQGYANATELADYLVAKGVPFREAHHIVGEAVVEAIAQGKPLEDLPLADLQKFSRVIAEDVYPILSL 427
                                             *********************************************************************** PP

                               TIGR00838 426 eeavekrdakGGtakeevekaieeakael 454
                                             +++++kr+akGG+++++v++ai+ ak++l
  lcl|FitnessBrowser__Koxy:BWI76_RS00855 428 QSCLDKRAAKGGVSPQQVAQAIADAKQRL 456
                                             **************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (457 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: 12.07
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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