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.24795.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 7.18
//
[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:

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