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

GapMind for Amino acid biosynthesis

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

Align arginosuccinate lyase (EC 4.3.2.1) (characterized)
to candidate CA265_RS18485 CA265_RS18485 argininosuccinate lyase

Query= reanno::Pedo557:CA265_RS18485
         (443 letters)



>FitnessBrowser__Pedo557:CA265_RS18485
          Length = 443

 Score =  880 bits (2275), Expect = 0.0
 Identities = 443/443 (100%), Positives = 443/443 (100%)

Query: 1   MKIWQKNIDVNQFVESFTVGKDRELDLQMAKFDVLGSLAHTQMLETINLLTAEELKTVQH 60
           MKIWQKNIDVNQFVESFTVGKDRELDLQMAKFDVLGSLAHTQMLETINLLTAEELKTVQH
Sbjct: 1   MKIWQKNIDVNQFVESFTVGKDRELDLQMAKFDVLGSLAHTQMLETINLLTAEELKTVQH 60

Query: 61  ELKNIYAEIEAGNFTIEDSVEDVHSQVEWLLTQRIGEAGKKIHSGRSRNDQVLVDLKLFF 120
           ELKNIYAEIEAGNFTIEDSVEDVHSQVEWLLTQRIGEAGKKIHSGRSRNDQVLVDLKLFF
Sbjct: 61  ELKNIYAEIEAGNFTIEDSVEDVHSQVEWLLTQRIGEAGKKIHSGRSRNDQVLVDLKLFF 120

Query: 121 RACIEDMVGQTSTLFNQLIELSNTHKDKLVPGYTHLQIAMPSSFGLWFGAYAESLADDME 180
           RACIEDMVGQTSTLFNQLIELSNTHKDKLVPGYTHLQIAMPSSFGLWFGAYAESLADDME
Sbjct: 121 RACIEDMVGQTSTLFNQLIELSNTHKDKLVPGYTHLQIAMPSSFGLWFGAYAESLADDME 180

Query: 181 LMLAAWKICNKNPLGSAAGYGSSFPLNRTLTTHLLGFETLNYNVVYAQMGRGKTERILAQ 240
           LMLAAWKICNKNPLGSAAGYGSSFPLNRTLTTHLLGFETLNYNVVYAQMGRGKTERILAQ
Sbjct: 181 LMLAAWKICNKNPLGSAAGYGSSFPLNRTLTTHLLGFETLNYNVVYAQMGRGKTERILAQ 240

Query: 241 AMSAVAATLAKMAMDVCLFINQNFGFISFPAELTTGSSIMPHKKNPDVFELIRSRCNKIQ 300
           AMSAVAATLAKMAMDVCLFINQNFGFISFPAELTTGSSIMPHKKNPDVFELIRSRCNKIQ
Sbjct: 241 AMSAVAATLAKMAMDVCLFINQNFGFISFPAELTTGSSIMPHKKNPDVFELIRSRCNKIQ 300

Query: 301 ALPNEIAMMITNLPSGYHRDLQLLKENLFPAITSLNECLEIATFMFQNITIKDDILKDKK 360
           ALPNEIAMMITNLPSGYHRDLQLLKENLFPAITSLNECLEIATFMFQNITIKDDILKDKK
Sbjct: 301 ALPNEIAMMITNLPSGYHRDLQLLKENLFPAITSLNECLEIATFMFQNITIKDDILKDKK 360

Query: 361 YDYLFSVEVVNDLALQGVPFREAYKIVGEQIENGSFAPSGQIHHTHEGSIGNLCNEQISA 420
           YDYLFSVEVVNDLALQGVPFREAYKIVGEQIENGSFAPSGQIHHTHEGSIGNLCNEQISA
Sbjct: 361 YDYLFSVEVVNDLALQGVPFREAYKIVGEQIENGSFAPSGQIHHTHEGSIGNLCNEQISA 420

Query: 421 AMQAVLSQFGFGKVNKAIEDLVK 443
           AMQAVLSQFGFGKVNKAIEDLVK
Sbjct: 421 AMQAVLSQFGFGKVNKAIEDLVK 443


Lambda     K      H
   0.320    0.134    0.388 

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: 807
Number of extensions: 18
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: 443
Length of database: 443
Length adjustment: 32
Effective length of query: 411
Effective length of database: 411
Effective search space:   168921
Effective search space used:   168921
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: 51 (24.3 bits)

Align candidate CA265_RS18485 CA265_RS18485 (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.29112.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   1.8e-105  339.5   0.1   2.2e-105  339.2   0.1    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS18485  CA265_RS18485 argininosuccinate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS18485  CA265_RS18485 argininosuccinate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  339.2   0.1  2.2e-105  2.2e-105      20     391 ..      22     392 ..       5     426 .. 0.94

  Alignments for each domain:
  == domain 1  score: 339.2 bits;  conditional E-value: 2.2e-105
                                  TIGR00838  20 slsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevkegklelevdaeDiHlavEr 87 
                                                  + D ++a+ D+ gs+aht++L++ ++lt+ee k ++++L++++ e+++g++++e+++eD+H++vE 
  lcl|FitnessBrowser__Pedo557:CA265_RS18485  22 DRELDLQMAKFDVLGSLAHTQMLETINLLTAEELKTVQHELKNIYAEIEAGNFTIEDSVEDVHSQVEW 89 
                                                456899************************************************************** PP

                                  TIGR00838  88 elidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalvekAekevetlmpgytHL 155
                                                 l++++g ++gkk+h+grsRnDqv +dl+l+ r+ +++++ +   l ++l+e+ +++++ l+pgytHL
  lcl|FitnessBrowser__Pedo557:CA265_RS18485  90 LLTQRIG-EAGKKIHSGRSRNDQVLVDLKLFFRACIEDMVGQTSTLFNQLIELSNTHKDKLVPGYTHL 156
                                                *******.************************************************************ PP

                                  TIGR00838 156 qrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidrellaelLgFdavvens 223
                                                q A P +++ ++ ayae+l+ D+e +l a k  nk+PlGs+A  g+sf+++r+l+++lLgF+++  n 
  lcl|FitnessBrowser__Pedo557:CA265_RS18485 157 QIAMPSSFGLWFGAYAESLADDMELMLAAWKICNKNPLGSAAGYGSSFPLNRTLTTHLLGFETLNYNV 224
                                                ******************************************************************** PP

                                  TIGR00838 224 ldavsdRDfiiElls.aaallmvhlsrlaEelilfsseEfgfvelsdevssgssimPqKKnpDvaEli 290
                                                ++a   R     +l+ a++ +++ l+++a ++ lf  ++fgf++++ e+++gssimP KKnpDv Eli
  lcl|FitnessBrowser__Pedo557:CA265_RS18485 225 VYAQMGRGKTERILAqAMSAVAATLAKMAMDVCLFINQNFGFISFPAELTTGSSIMPHKKNPDVFELI 292
                                                *******98876665145778899******************************************** PP

                                  TIGR00838 291 RgktgrviGnltglltilKalPlaYnkDlqEdkealfdalktveellevvtgllkelkvnkerleeaa 358
                                                R+++ +++     + +++  lP+ Y +Dlq  ke+lf a++ ++e+le++t+++++++++ + l +  
  lcl|FitnessBrowser__Pedo557:CA265_RS18485 293 RSRCNKIQALPNEIAMMITNLPSGYHRDLQLLKENLFPAITSLNECLEIATFMFQNITIKDDIL-KDK 359
                                                ********99999999999*****************************************9995.556 PP

                                  TIGR00838 359 kknfalatdlAdylvrkGvPFReaheivGevva 391
                                                k ++    ++ + l+ +GvPFRea++ivGe ++
  lcl|FitnessBrowser__Pedo557:CA265_RS18485 360 KYDYLFSVEVVNDLALQGVPFREAYKIVGEQIE 392
                                                899**************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (443 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: 0.02u 0.02s 00:00:00.04 Elapsed: 00:00:00.02
# Mc/sec: 7.45
//
[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