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

GapMind for Amino acid biosynthesis

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

Align asparagine synthase (glutamine-hydrolysing) 1; EC 6.3.5.4 (characterized)
to candidate CA265_RS07955 CA265_RS07955 asparagine synthase (glutamine-hydrolyzing)

Query= CharProtDB::CH_005185
         (632 letters)



>FitnessBrowser__Pedo557:CA265_RS07955
          Length = 613

 Score =  309 bits (792), Expect = 2e-88
 Identities = 197/623 (31%), Positives = 312/623 (50%), Gaps = 40/623 (6%)

Query: 1   MCGFVGVFNKHPLAQTADQEELIKQMNQMIVHRGPDSDGYFHDEHVGFGFRRLSIIDVE- 59
           MCG  G    +        + ++++    I  RGPD  G    + V F   RL+IID++ 
Sbjct: 1   MCGIYGTTIPY-------SDGIVREKMARISFRGPDYTGVQRYDQVIFAHNRLAIIDLDA 53

Query: 60  NGGQPLSYEDETYWIIFNGEIYNYIELREELEAKGYTFNTDSDTEVLLATYRHYKEEAAS 119
              QP SY      I+FNGEIYNY ++R ELE K Y FNT SDTEV+ A Y  Y     +
Sbjct: 54  RSNQPFSYMH--LHIVFNGEIYNYKDIRRELERKNYQFNTSSDTEVICAAYLEYGAGCLT 111

Query: 120 KLRGMFAFLIWNKNDHVLYGARDPFGIKPLYYTTINDQVYFASERKSLMVAQNDIEIDKE 179
           +  GMFAF+I++   + L+GARD FG KP YY   +    FAS+   + +    + +++E
Sbjct: 112 RFNGMFAFVIYDTRKNELFGARDRFGKKPFYYAHDHSSFEFASQPSQINI-DRGLSVNEE 170

Query: 180 ALQQYMSFQFVPEPSTLDAHVKKVEPGSQFTIRPDG-----------DITFKTYFKANFK 228
           A+ QY+ + +VPEP ++ A VK++     F                 D  +K  F+ ++ 
Sbjct: 171 AINQYLIWGYVPEPQSIYAEVKQLPAAHYFKYDLKSHKLKITEYWTLDYGWKNKFEGSY- 229

Query: 229 PVQTEEDKLVKEVRDAIYDSVNVHMRSDVPVGSFLSGGIDSSFIVSVAKEFHPSLKTFSV 288
               EE K  + +   + D+V + M +DVP+G FLSGGIDSS I ++A +    +KTFS+
Sbjct: 230 ----EEAK--EALALILADAVKIRMNADVPLGVFLSGGIDSSLIAALATKEIDHVKTFSI 283

Query: 289 GFEQQGFSEVDVAKETAAALGIENISKVISPEEYMNELPKIVWHFDDPLADPAAIPLYFV 348
            F ++GF E   A + A  LG ++ +   +  + +  +      +D+P AD +AIP   +
Sbjct: 284 KFNEKGFDESAYASQVAKHLGTDHYTIECNYNDGIELIENFNRFYDEPFADSSAIPTMLL 343

Query: 349 AKEAKKHVTVALSGEGADELFGGYNIYREPLSLKPFERIPSGLKKMLLHVAAVMPEGMRG 408
           +K  +KHVTVALSG+  DE F GY+ Y+    +      P G++K L  +    P     
Sbjct: 344 SKNTRKHVTVALSGDAGDEAFLGYHRYKWIKQVNSLFYAPHGVRKALAGLINQSPSYRHK 403

Query: 409 KSLLERGCTPLQDRYIGNAKIFEES-VKKQLLKHYNPNLSYRDVTKTYFTESSSYSDINK 467
              +      ++  Y+      E S VK+  L  YNP +        +   + S   + +
Sbjct: 404 LIAMGISMEDVEKLYVKMFGNMENSWVKQPDLAKYNPLM--------HILANPSKPLLER 455

Query: 468 MQYVDIHTWMRGDILLKADKMTMANSLELRVPFLDKVVFDVASKIPDELKTKNGTTKYLL 527
           +   DI T++ GDI  K D+ +MA SLE R P +D  V + +  +P   K  NG  K +L
Sbjct: 456 ISDFDIKTYLNGDINTKVDRASMAFSLESRSPLMDYRVMEFSRSLPTAFKYTNGNQKRIL 515

Query: 528 RKAAEGIVPEHVLNRKKLGFPVPIRHWLKNEMNEWVRNIIQESQTDAY--IHKDYVLQLL 585
           +      VP H+ +R K GF +P +HW +NE+ ++V + +          IH     +++
Sbjct: 516 KDLLFDHVPAHMFDRPKAGFTMPFQHWFRNELKDYVMDNLSADNLKNIPGIHLKRTQEII 575

Query: 586 EDHCADKADNSRKIWTVLIFMIW 608
            +H   K +   +IW +L+   W
Sbjct: 576 NEHMTGKWNRYPQIWKLLVLSQW 598


Lambda     K      H
   0.319    0.136    0.403 

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: 1024
Number of extensions: 49
Number of successful extensions: 6
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: 632
Length of database: 613
Length adjustment: 37
Effective length of query: 595
Effective length of database: 576
Effective search space:   342720
Effective search space used:   342720
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 (21.7 bits)
S2: 54 (25.4 bits)

Align candidate CA265_RS07955 CA265_RS07955 (asparagine synthase (glutamine-hydrolyzing))
to HMM TIGR01536 (asnB: asparagine synthase (glutamine-hydrolyzing) (EC 6.3.5.4))

# 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/TIGR01536.hmm
# target sequence database:        /tmp/gapView.6735.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01536  [M=517]
Accession:   TIGR01536
Description: asn_synth_AEB: asparagine synthase (glutamine-hydrolyzing)
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   2.4e-134  435.1   0.0   2.8e-134  434.8   0.0    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS07955  CA265_RS07955 asparagine synthas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS07955  CA265_RS07955 asparagine synthase (glutamine-hydrolyzing)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  434.8   0.0  2.8e-134  2.8e-134      18     517 .]      14     535 ..       2     535 .. 0.87

  Alignments for each domain:
  == domain 1  score: 434.8 bits;  conditional E-value: 2.8e-134
                                  TIGR01536  18 eaikemletlahRGPDaegvwkdekeenailghrRLaiidlseg.aQPlsnekevvivfnGEIYNhee 84 
                                                  ++e + +++ RGPD +gv +   ++++i++h+RLaiidl +  +QP+s+ +   ivfnGEIYN+++
  lcl|FitnessBrowser__Pedo557:CA265_RS07955  14 GIVREKMARISFRGPDYTGVQR---YDQVIFAHNRLAIIDLDARsNQPFSYMH-LHIVFNGEIYNYKD 77 
                                                4555667889*********755...59***************999*******9.68************ PP

                                  TIGR01536  85 LreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelflaRDrlGikPLYyas 152
                                                +r+ele+k y+F+t sDtEVi aay e+g  ++ r++GmFAf+++d++k+elf aRDr+G+kP+Yya 
  lcl|FitnessBrowser__Pedo557:CA265_RS07955  78 IRRELERKNYQFNTSSDTEVICAAYLEYGAGCLTRFNGMFAFVIYDTRKNELFGARDRFGKKPFYYAH 145
                                                ******************************************************************** PP

                                  TIGR01536 153 eqgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkelepakal.....dgeekl 215
                                                +++++ faS    +        ++++ea+ ++l   +vp+++++++evk+l++a+++     +++ k+
  lcl|FitnessBrowser__Pedo557:CA265_RS07955 146 DHSSFEFASQPSQINIDR--GLSVNEEAINQYLIWGYVPEPQSIYAEVKQLPAAHYFkydlkSHKLKI 211
                                                *********998876554..6899*********************************88776556666 PP

                                  TIGR01536 216 eeywevekee...vkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslvaaiakkeaksev 280
                                                 eyw +++     ++ s ee++e l   l davk r+ advp+gv+lSGG+DSsl+aa+a ke++ +v
  lcl|FitnessBrowser__Pedo557:CA265_RS07955 212 TEYWTLDYGWknkFEGSYEEAKEALALILADAVKIRMNADVPLGVFLSGGIDSSLIAALATKEID-HV 278
                                                67****9865555999*************************************************.8* PP

                                  TIGR01536 281 ktFsigfedskdldeskaarkvadelgtehkevliseeevlkeleevilaleeptairasiplyllsk 348
                                                ktFsi+f+ +k +des++a++va++lgt+h++++ + +++++ +e+  +  +ep+a++++ip+ llsk
  lcl|FitnessBrowser__Pedo557:CA265_RS07955 279 KTFSIKFN-EKGFDESAYASQVAKHLGTDHYTIECNYNDGIELIENFNRFYDEPFADSSAIPTMLLSK 345
                                                ********.*********************************************************** PP

                                  TIGR01536 349 larekgvkVvLsGeGaDElfgGYeyfreakaeeale.........lpease......laekklllqak 401
                                                 +r++ v+V+LsG+ +DE f GY++++  k+ + l          l            +++++l++  
  lcl|FitnessBrowser__Pedo557:CA265_RS07955 346 NTRKH-VTVALSGDAGDEAFLGYHRYKWIKQVNSLFyaphgvrkaL----AglinqsPSYRHKLIAMG 408
                                                *****.*********************9988887765555544442....032223333444466666 PP

                                  TIGR01536 402 lakeselkellkakleeelkekeelkkelkee............seleellrldlelllsdllrak.D 456
                                                +  e ++k ++k+    +++++  ++ +l++               le++ + d++++l+++++ k D
  lcl|FitnessBrowser__Pedo557:CA265_RS07955 409 ISMEDVEKLYVKM--FGNMENSWVKQPDLAKYnplmhilanpskPLLERISDFDIKTYLNGDINTKvD 474
                                                6666666666653..3333333333333333334467888888799********************** PP

                                  TIGR01536 457 rvsmahslEvRvPflDkelvelalsippelklrdgkeKvlLreaaeellPeeileRkKeaf 517
                                                r+sma slE+R P++D +++e+  s+p+  k  +g++K++L+ ++ +++P ++ +R+K++f
  lcl|FitnessBrowser__Pedo557:CA265_RS07955 475 RASMAFSLESRSPLMDYRVMEFSRSLPTAFKYTNGNQKRILKDLLFDHVPAHMFDRPKAGF 535
                                                ***********************************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (613 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: 00:00:00.03
# Mc/sec: 9.19
//
[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