Alignments for a candidate for ans in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for ans in Klebsiella michiganensis M5al

Align L-asparaginase subunit (EC 3.5.1.38) (characterized)
to candidate BWI76_RS11360 BWI76_RS11360 L-asparaginase

Query= metacyc::MONOMER-13049
         (346 letters)



>FitnessBrowser__Koxy:BWI76_RS11360
          Length = 347

 Score =  506 bits (1302), Expect = e-148
 Identities = 255/345 (73%), Positives = 293/345 (84%)

Query: 2   FNALFVVVFVCFSSLANAAENLPNIVILATGGTIAGSAAANTQTTGYKAGALGVETLIQA 61
           F AL  +  +  S+ A +   LP+IVILATGGTIAGSAA+NTQTTGYKAGA+GV+TLI A
Sbjct: 3   FRALLAITLLTISAFAFSDTRLPHIVILATGGTIAGSAASNTQTTGYKAGAIGVQTLINA 62

Query: 62  VPELKTLANIKGEQVASIGSENMTSDVLLTLSKRVNELLARSDVDGVVITHGTDTLDESP 121
           VPE+  +A + GEQVA+IGSENMTSD++L LSKRVNELLAR DVDGVVITHGTDTLDE+P
Sbjct: 63  VPEMSKVARVDGEQVANIGSENMTSDIILKLSKRVNELLARDDVDGVVITHGTDTLDETP 122

Query: 122 YFLNLTVKSDKPVVFVAAMRPATAISADGPMNLYGAVKVAADKNSRGRGVLVVLNDRIGS 181
           YFLNLTVKS+KPVVF AAMRPATAISADGPMNL  AV VAAD  ++GRGV+VVLNDRIG+
Sbjct: 123 YFLNLTVKSNKPVVFTAAMRPATAISADGPMNLLEAVTVAADPQAKGRGVMVVLNDRIGA 182

Query: 182 ARFISKTNASTLDTFKAPEEGYLGVIIGDKIYYQTRLDKVHTTRSVFDVTNVDKLPAVDI 241
           ARF++KTNA+TLDTFKAPEEGYLGVI+  K  ++TR+DK+HT RSVFDV  ++ LP V I
Sbjct: 183 ARFVTKTNATTLDTFKAPEEGYLGVIVSGKPQFETRVDKIHTVRSVFDVRQLNALPKVVI 242

Query: 242 IYGYQDDPEYMYDASIKHGVKGIVYAGMGAGSVSKRGDAGIRKAESKGIVVVRSSRTGSG 301
           IYGYQDDPEYMYDA+I H V GI+YAG GAGSVS R  AGI KAE  GIVVVR+SRTGSG
Sbjct: 243 IYGYQDDPEYMYDAAIAHHVDGIIYAGTGAGSVSVRSAAGIEKAEKAGIVVVRASRTGSG 302

Query: 302 IVPPDAGQPGLVADSLSPAKSRILLMLALTKTTNPAVIQDYFHAY 346
           +VP D GQPGLV+DSL+PAK+RILLM ALT+T NP VIQ YFH Y
Sbjct: 303 VVPVDDGQPGLVSDSLNPAKARILLMTALTQTKNPQVIQQYFHTY 347


Lambda     K      H
   0.316    0.133    0.369 

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: 436
Number of extensions: 12
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: 346
Length of database: 347
Length adjustment: 29
Effective length of query: 317
Effective length of database: 318
Effective search space:   100806
Effective search space used:   100806
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate BWI76_RS11360 BWI76_RS11360 (L-asparaginase)
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.25889.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   3.9e-138  446.1   4.3   4.3e-138  445.9   4.3    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS11360  BWI76_RS11360 L-asparaginase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS11360  BWI76_RS11360 L-asparaginase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  445.9   4.3  4.3e-138  4.3e-138       7     352 .]       7     347 .]       1     347 [] 0.97

  Alignments for each domain:
  == domain 1  score: 445.9 bits;  conditional E-value: 4.3e-138
                               TIGR00520   7 aalaavvlkvsaakaksLPnikilatGGtiagkgqssastaeYkvgklgvedLieavPelkeianiegeqi 77 
                                              a++++++++ a  ++ LP+i ilatGGtiag+++s+++t++Yk+g +gv++Li+avPe++++a+++geq+
  lcl|FitnessBrowser__Koxy:BWI76_RS11360   7 LAITLLTISAFAFSDTRLPHIVILATGGTIAGSAASNTQTTGYKAGAIGVQTLINAVPEMSKVARVDGEQV 77 
                                             5677788888888999******************************************************* PP

                               TIGR00520  78 vnvgsqdlneevllklakrisealasddvdGivithGtDtleetayfldltvksdkPvvlvGamRpatsvs 148
                                             +n+gs+++  +++lkl kr++e la ddvdG+vithGtDtl+et yfl+ltvks+kPvv+  amRpat++s
  lcl|FitnessBrowser__Koxy:BWI76_RS11360  78 ANIGSENMTSDIILKLSKRVNELLARDDVDGVVITHGTDTLDETPYFLNLTVKSNKPVVFTAAMRPATAIS 148
                                             *********************************************************************** PP

                               TIGR00520 149 aDGplnLYnavsvaadeksagrGvlvvlndrilsarevtktnttsldtfkseeqGalGyiandkieyerep 219
                                             aDGp+nL +av+vaad++++grGv+vvlndri  ar vtktn+t+ldtfk+ e+G+lG i+ +k ++e+++
  lcl|FitnessBrowser__Koxy:BWI76_RS11360 149 ADGPMNLLEAVTVAADPQAKGRGVMVVLNDRIGAARFVTKTNATTLDTFKAPEEGYLGVIVSGKPQFETRV 219
                                             *********************************************************************** PP

                               TIGR00520 220 vkkhtletefdvskldeplPkvdiiYayqnlpeelvkavvdagakGivlagvGnGslsaaalkvleeaake 290
                                              k ht+ + fdv++l+  lPkv iiY+yq+ pe++ +a++ ++ +Gi+ ag+G+Gs+s       e+a k 
  lcl|FitnessBrowser__Koxy:BWI76_RS11360 220 DKIHTVRSVFDVRQLNA-LPKVVIIYGYQDDPEYMYDAAIAHHVDGIIYAGTGAGSVSVRSAAGIEKAEKA 289
                                             *****************.***************************************************** PP

                               TIGR00520 291 svvivrssRvadGvvtkdaevddkealiasgtLnPqkaRvLLqLaLtktkdlekiqevfeey 352
                                             ++v+vr+sR+ +Gvv+    vdd++  + s++LnP kaR+LL+ aLt+tk+++ iq++f+ y
  lcl|FitnessBrowser__Koxy:BWI76_RS11360 290 GIVVVRASRTGSGVVP----VDDGQPGLVSDSLNPAKARILLMTALTQTKNPQVIQQYFHTY 347
                                             ****************....556667789******************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (352 nodes)
Target sequences:                          1  (347 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: 6.94
//
[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