Alignments for a candidate for argH in Bacteroides thetaiotaomicron VPI-5482

GapMind for Amino acid biosynthesis

Alignments for a candidate for argH in Bacteroides thetaiotaomicron VPI-5482

Align arginosuccinate lyase (EC 4.3.2.1) (characterized)
to candidate 353259 BT3733 argininosuccinate lyase (NCBI ptt file)

Query= reanno::Btheta:353259
         (446 letters)



>FitnessBrowser__Btheta:353259
          Length = 446

 Score =  889 bits (2296), Expect = 0.0
 Identities = 446/446 (100%), Positives = 446/446 (100%)

Query: 1   MAQKLWEKSVQVNKDIERFTVGRDREMDLYLAKHDVLGSMAHITMLESIGLLTKEELEQL 60
           MAQKLWEKSVQVNKDIERFTVGRDREMDLYLAKHDVLGSMAHITMLESIGLLTKEELEQL
Sbjct: 1   MAQKLWEKSVQVNKDIERFTVGRDREMDLYLAKHDVLGSMAHITMLESIGLLTKEELEQL 60

Query: 61  LAELKTIYASVERGEFIIEEGVEDVHSQVELMLTRRLGDVGKKIHSGRSRNDQVLLDLKL 120
           LAELKTIYASVERGEFIIEEGVEDVHSQVELMLTRRLGDVGKKIHSGRSRNDQVLLDLKL
Sbjct: 61  LAELKTIYASVERGEFIIEEGVEDVHSQVELMLTRRLGDVGKKIHSGRSRNDQVLLDLKL 120

Query: 121 FTRTQIREIAEAVEQLFHVLILQSERYKNVLMPGYTHLQIAMPSSFGLWFGAYAESLVDD 180
           FTRTQIREIAEAVEQLFHVLILQSERYKNVLMPGYTHLQIAMPSSFGLWFGAYAESLVDD
Sbjct: 121 FTRTQIREIAEAVEQLFHVLILQSERYKNVLMPGYTHLQIAMPSSFGLWFGAYAESLVDD 180

Query: 181 MQFLQAAFRMCNRNPLGSAAGYGSSFPLNRTMTTDLLGFDSLNYNVVYAQMGRGKLERNV 240
           MQFLQAAFRMCNRNPLGSAAGYGSSFPLNRTMTTDLLGFDSLNYNVVYAQMGRGKLERNV
Sbjct: 181 MQFLQAAFRMCNRNPLGSAAGYGSSFPLNRTMTTDLLGFDSLNYNVVYAQMGRGKLERNV 240

Query: 241 AFALATIAGTISKLAFDACMFNSQNFGFVKLPDDCTTGSSIMPHKKNPDVFELTRAKCNK 300
           AFALATIAGTISKLAFDACMFNSQNFGFVKLPDDCTTGSSIMPHKKNPDVFELTRAKCNK
Sbjct: 241 AFALATIAGTISKLAFDACMFNSQNFGFVKLPDDCTTGSSIMPHKKNPDVFELTRAKCNK 300

Query: 301 LQSLPQQIMMIANNLPSGYFRDLQIIKEVFLPAFQELKDCLQMTTYIMNEIKVNEHILDD 360
           LQSLPQQIMMIANNLPSGYFRDLQIIKEVFLPAFQELKDCLQMTTYIMNEIKVNEHILDD
Sbjct: 301 LQSLPQQIMMIANNLPSGYFRDLQIIKEVFLPAFQELKDCLQMTTYIMNEIKVNEHILDD 360

Query: 361 DKYLFIFSVEEVNRLAREGMPFRDAYKKVGLDIEAGKFTHDKQVHHTHEGSIGNLCNDEI 420
           DKYLFIFSVEEVNRLAREGMPFRDAYKKVGLDIEAGKFTHDKQVHHTHEGSIGNLCNDEI
Sbjct: 361 DKYLFIFSVEEVNRLAREGMPFRDAYKKVGLDIEAGKFTHDKQVHHTHEGSIGNLCNDEI 420

Query: 421 SALMQQVVDGFNFCGMEQAEKALLGR 446
           SALMQQVVDGFNFCGMEQAEKALLGR
Sbjct: 421 SALMQQVVDGFNFCGMEQAEKALLGR 446


Lambda     K      H
   0.322    0.137    0.395 

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: 797
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: 446
Length of database: 446
Length adjustment: 32
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 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (24.3 bits)

Align candidate 353259 BT3733 (argininosuccinate lyase (NCBI ptt file))
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.1250.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   8.7e-107  343.8   0.2     1e-106  343.6   0.2    1.0  1  lcl|FitnessBrowser__Btheta:353259  BT3733 argininosuccinate lyase (


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:353259  BT3733 argininosuccinate lyase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  343.6   0.2    1e-106    1e-106      20     388 ..      24     391 ..       5     429 .. 0.93

  Alignments for each domain:
  == domain 1  score: 343.6 bits;  conditional E-value: 1e-106
                          TIGR00838  20 slsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevkegklelevdaeDiHlavErelidkvge 95 
                                          + D  la++D+ gs+ah ++L+  g+lt+ee ++l ++L++++ +v++g++ +e+ +eD+H++vE +l+ ++g 
  lcl|FitnessBrowser__Btheta:353259  24 DREMDLYLAKHDVLGSMAHITMLESIGLLTKEELEQLLAELKTIYASVERGEFIIEEGVEDVHSQVELMLTRRLG- 98 
                                        4578999********************************************************************. PP

                          TIGR00838  96 dvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalvekAekevetlmpgytHLqrAqPitlaHhllaya 171
                                        dvgkk+h+grsRnDqv  dl+l+ r +++e+aea+++l ++l+ + e+ +++lmpgytHLq A P +++ ++ aya
  lcl|FitnessBrowser__Btheta:353259  99 DVGKKIHSGRSRNDQVLLDLKLFTRTQIREIAEAVEQLFHVLILQSERYKNVLMPGYTHLQIAMPSSFGLWFGAYA 174
                                        **************************************************************************** PP

                          TIGR00838 172 emlerDleRlldalkRvnksPlGsgAlagtsfeidrellaelLgFdavvensldavsdRDfii.Ellsaaallmvh 246
                                        e+l  D++ l+ a++  n++PlGs+A  g+sf+++r+++++lLgFd++  n ++a   R  +  ++ +a+a ++  
  lcl|FitnessBrowser__Btheta:353259 175 ESLVDDMQFLQAAFRMCNRNPLGSAAGYGSSFPLNRTMTTDLLGFDSLNYNVVYAQMGRGKLErNVAFALATIAGT 250
                                        ***********************************************************98752577999****** PP

                          TIGR00838 247 lsrlaEelilfsseEfgfvelsdevssgssimPqKKnpDvaEliRgktgrviGnltglltilKalPlaYnkDlqEd 322
                                        +s+la +  +f+s++fgfv+l+d++++gssimP KKnpDv El R+k+ +++   + +++i   lP+ Y +Dlq +
  lcl|FitnessBrowser__Btheta:353259 251 ISKLAFDACMFNSQNFGFVKLPDDCTTGSSIMPHKKNPDVFELTRAKCNKLQSLPQQIMMIANNLPSGYFRDLQII 326
                                        **************************************************************************** PP

                          TIGR00838 323 kealfdalktveellevvtgllkelkvnkerleeaakknfalatdlAdylvrkGvPFReaheivGe 388
                                        ke +  a ++++++l++ t +++e+kvn++   +  k  f    +  + l+r+G+PFR+a++ vG 
  lcl|FitnessBrowser__Btheta:353259 327 KEVFLPAFQELKDCLQMTTYIMNEIKVNEHI-LDDDKYLFIFSVEEVNRLAREGMPFRDAYKKVGL 391
                                        ****************************998.666788899999999***************9995 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (446 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.42
//
[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