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

GapMind for catabolism of small carbon sources

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

Align asparaginase (EC 3.5.1.1) (characterized)
to candidate 352284 BT2757 L-asparaginase II precursor (NCBI ptt file)

Query= BRENDA::P00805
         (348 letters)



>FitnessBrowser__Btheta:352284
          Length = 352

 Score =  411 bits (1057), Expect = e-119
 Identities = 217/352 (61%), Positives = 262/352 (74%), Gaps = 4/352 (1%)

Query: 1   MEFFKKTALAALVMGFSG--AALALPNITILATGGTIAGGGDSATKSNYTVGKVGVENLV 58
           M+  KK  L  + +  S   A  A PNI ILATGGTIAG G SAT ++YT G+V +  L+
Sbjct: 1   MKQIKKLGLVVVTLLLSATMAFAAKPNIHILATGGTIAGTGSSATGTSYTAGQVAIGALL 60

Query: 59  NAVPQLKDIANVKGEQVVNIGSQDMNDNVWLTLAKKINTDCDKTD--GFVITHGTDTMEE 116
           +AVP++KDIANV GEQ+V IGSQDMND VWLTLAKKIN    + D  G VITHGTDTMEE
Sbjct: 61  DAVPEIKDIANVTGEQIVRIGSQDMNDEVWLTLAKKINELLKRPDIDGIVITHGTDTMEE 120

Query: 117 TAYFLDLTVKCDKPVVMVGAMRPSTSMSADGPFNLYNAVVTAADKASANRGVLVVMNDTV 176
           TAYFL+LTVK DKPVV+VGAMRPST++SADGP NLYNAVVTAA K S ++GVLV MN  +
Sbjct: 121 TAYFLNLTVKSDKPVVLVGAMRPSTALSADGPLNLYNAVVTAAAKESKDKGVLVAMNGLI 180

Query: 177 LDGRDVTKTNTTDVATFKSVNYGPLGYIHNGKIDYQRTPARKHTSDTPFDVSKLNELPKV 236
           L    V K NT DV TF++ N G LGY+ NGK+ Y +   +KHT+ + FDV+KL  LPKV
Sbjct: 181 LGAESVVKMNTVDVQTFQAPNSGALGYVLNGKVCYNQITLKKHTTQSVFDVTKLTSLPKV 240

Query: 237 GIVYNYANASDLPAKALVDAGYDGIVSAGVGNGNLYKSVFDTLATAAKTGTAVVRSSRVP 296
           GIVY+Y+N        L++ GY GI+ AGVGNGN++K++F +L  A + G  VVRSSRVP
Sbjct: 241 GIVYSYSNIEADMMTPLLNNGYKGIIHAGVGNGNIHKNIFPSLIDARRKGIVVVRSSRVP 300

Query: 297 TGATTQDAEVDDAKYGFVASGTLNPQKARVLLQLALTQTKDPQQIQQIFNQY 348
           TG TT DAEVDDAKY FVAS  LNPQK+RVLL LALT+T D +QIQ+ FN+Y
Sbjct: 301 TGPTTLDAEVDDAKYQFVASQELNPQKSRVLLMLALTKTTDWKQIQEYFNEY 352


Lambda     K      H
   0.314    0.130    0.368 

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: 362
Number of extensions: 12
Number of successful extensions: 2
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: 348
Length of database: 352
Length adjustment: 29
Effective length of query: 319
Effective length of database: 323
Effective search space:   103037
Effective search space used:   103037
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 49 (23.5 bits)

Align candidate 352284 BT2757 (L-asparaginase II precursor (NCBI ptt file))
to HMM TIGR00520 (L-asparaginase, type II (EC 3.5.1.1))

# 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.carbon/TIGR00520.hmm
# target sequence database:        /tmp/gapView.23416.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00520  [M=352]
Accession:   TIGR00520
Description: asnASE_II: L-asparaginase, type II
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   9.4e-150  484.3   6.1     1e-149  484.1   6.1    1.0  1  lcl|FitnessBrowser__Btheta:352284  BT2757 L-asparaginase II precurs


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:352284  BT2757 L-asparaginase II precursor (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  484.1   6.1    1e-149    1e-149      18     352 .]      19     352 .]       1     352 [] 0.96

  Alignments for each domain:
  == domain 1  score: 484.1 bits;  conditional E-value: 1e-149
                          TIGR00520  18 aakaksLPnikilatGGtiagkgqssastaeYkvgklgvedLieavPelkeianiegeqivnvgsqdlneevllkl 93 
                                        ++  ++ Pni+ilatGGtiag+g+s a+ ++Y++g++++  L++avPe+k+ian+ geqiv++gsqd+n+ev+l+l
  lcl|FitnessBrowser__Btheta:352284  19 TMAFAAKPNIHILATGGTIAGTGSS-ATGTSYTAGQVAIGALLDAVPEIKDIANVTGEQIVRIGSQDMNDEVWLTL 93 
                                        3335778****************99.9************************************************* PP

                          TIGR00520  94 akrisealasddvdGivithGtDtleetayfldltvksdkPvvlvGamRpatsvsaDGplnLYnavsvaadeksag 169
                                        ak+i+e l+  d+dGivithGtDt+eetayfl+ltvksdkPvvlvGamRp+t++saDGplnLYnav++aa+++s++
  lcl|FitnessBrowser__Btheta:352284  94 AKKINELLKRPDIDGIVITHGTDTMEETAYFLNLTVKSDKPVVLVGAMRPSTALSADGPLNLYNAVVTAAAKESKD 169
                                        **************************************************************************** PP

                          TIGR00520 170 rGvlvvlndrilsarevtktnttsldtfkseeqGalGyiandkieyerepvkkhtletefdvskldeplPkvdiiY 245
                                        +Gvlv++n  il+a  v+k+nt +++tf++ ++GalGy+ n+k+ y++  +kkht+++ fdv kl++ lPkv+i+Y
  lcl|FitnessBrowser__Btheta:352284 170 KGVLVAMNGLILGAESVVKMNTVDVQTFQAPNSGALGYVLNGKVCYNQITLKKHTTQSVFDVTKLTS-LPKVGIVY 244
                                        *******************************************************************.******** PP

                          TIGR00520 246 ayqnlpeelvkavvdagakGivlagvGnGslsaaalkvleeaakesvvivrssRvadGvvtkdaevddk.ealias 320
                                        +y+n+  +++  ++++g+kGi+ agvGnG+++++ +  l +a ++++v+vrssRv++G +t daevdd+ ++++as
  lcl|FitnessBrowser__Btheta:352284 245 SYSNIEADMMTPLLNNGYKGIIHAGVGNGNIHKNIFPSLIDARRKGIVVVRSSRVPTGPTTLDAEVDDAkYQFVAS 320
                                        ********************************************************************99****** PP

                          TIGR00520 321 gtLnPqkaRvLLqLaLtktkdlekiqevfeey 352
                                        ++LnPqk+RvLL+LaLtkt d ++iqe+f+ey
  lcl|FitnessBrowser__Btheta:352284 321 QELNPQKSRVLLMLALTKTTDWKQIQEYFNEY 352
                                        ******************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (352 nodes)
Target sequences:                          1  (352 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: 10.09
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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

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 catabolism of small carbon sources