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.11535.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: 11.39
//
[ok]

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

Links

Downloads

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:

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