Alignments for a candidate for asnB in Dechloromonas agitata is5

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Dechloromonas agitata is5

Align asparagine synthase (glutamine-hydrolysing) 1; EC 6.3.5.4 (characterized)
to candidate WP_027458901.1 K420_RS0115800 XrtA/PEP-CTERM system amidotransferase

Query= CharProtDB::CH_005185
         (632 letters)



>NCBI__GCF_000519045.1:WP_027458901.1
          Length = 635

 Score =  336 bits (862), Expect = 2e-96
 Identities = 207/626 (33%), Positives = 337/626 (53%), Gaps = 28/626 (4%)

Query: 1   MCGFVGVFNKHPLAQTADQEELIKQMNQMIVHRGPDSDGYFHDEHVGFGFRRLSIIDVEN 60
           MCG  G+F+    ++      ++ +MN+   HRGPD  G   +  +G G RRLSIID+  
Sbjct: 1   MCGITGIFDTR--SRRDIDRAVLHRMNEAQFHRGPDEGGLHIEPGLGLGHRRLSIIDLST 58

Query: 61  GGQPLSYEDETYWIIFNGEIYNYIELREELEAKGYTFNTDSDTEVLLATYRHYKEEAASK 120
           G QPL  ED++  ++FNGEIYNY EL  EL+A G+ F+T SDTEV++  +  + E    +
Sbjct: 59  GQQPLYNEDKSVCVVFNGEIYNYQELIPELQALGHVFHTRSDTEVIVHAWEAWGERCVDR 118

Query: 121 LRGMFAFLIWNKNDHVLYGARDPFGIKPLYYTTINDQVY-FASERKSLMVAQN-DIEIDK 178
            RGMFAF +W++N   L+ ARD  G+KPL+Y  ++D  + F SE KSL+       +ID 
Sbjct: 119 FRGMFAFALWDRNRETLFLARDRLGVKPLFYALLDDGSFLFGSELKSLLAHGGLKRDIDP 178

Query: 179 EALQQYMSFQFVPEPSTLDAHVKKVEPGSQFTIRPDGDI-TFKTYFKANF---KPVQTEE 234
            A+++Y +  +V EP  +    +K+ P     +R    +   + Y+   F    P+   +
Sbjct: 179 CAVEEYFALGYVAEPRAIFKQARKLPPACTLLLRRGQPVGQPREYWDVRFTLDNPISDAD 238

Query: 235 DKLVKEVRDAIYDSVNVHMRSDVPVGSFLSGGIDSSFIVSVAKEFHPS-LKTFSVGFEQQ 293
            +   E+   + +S+ + M S+VP+G+FLSGG+DSS +V++      + + T S+GF   
Sbjct: 239 AQ--AELTHRLEESIKLRMISEVPLGAFLSGGVDSSAVVAMMAGLSANPVNTCSIGFSDP 296

Query: 294 GFSEVDVAKETAAALGIENISKVISPEEYMNELPKIVWHFDDPLADPAAIPLYFVAKEAK 353
            F+E + A+  A      +   V+  +++ + +  +   +D+P AD +AIP Y V + A+
Sbjct: 297 AFNESEFARMVADRYHTNHHLDVVESDDF-DLIDTLARLYDEPYADSSAIPTYRVCQLAR 355

Query: 354 KHVTVALSGEGADELFGGYNIYR-EPLSLKPFERIPSGLKKMLLHVAAVM-------PEG 405
           KHVTVALSG+G DE FGGY  Y+   +  K    +P GL++ L      +       P  
Sbjct: 356 KHVTVALSGDGGDESFGGYRRYKLHLMEEKMRSALPLGLRRPLFGTLGKLYPKADWAPRV 415

Query: 406 MRGKSLLERGCTPLQDRYIGNAKIFEESVKKQLLK-HYNPNLSYRDVTKTYFTESSSYSD 464
            R K+  E       + Y  +  I    ++ QL    +   L   D  +  FT+ ++ +D
Sbjct: 416 FRAKTTFEGIARSSVEGYFHSVSILRAPMRNQLFSPQFKAALGGYDALQV-FTDHAAKAD 474

Query: 465 ----INKMQYVDIHTWMRGDILLKADKMTMANSLELRVPFLDKVVFDVASKIPDELKTKN 520
               +  +QY+D+ T++ GDI  K D+ +MA+SLE+R P +D  + +  + +P   K + 
Sbjct: 475 TQDPLALIQYLDLKTYLIGDINTKVDRASMAHSLEVREPLMDHKLVEWLATLPSTQKIRG 534

Query: 521 GTTKYLLRKAAEGIVPEHVLNRKKLGFPVPIRHWLKNEMNEWVRNIIQESQ--TDAYIHK 578
              KYLL+KA E  +P  VL R K+GF VP+  W +  +   V+  I  S+     + ++
Sbjct: 535 QEGKYLLKKAMEPHLPNDVLYRPKMGFSVPLARWFRGPLKARVQESILGSRLADTGWFNR 594

Query: 579 DYVLQLLEDHCADKADNSRKIWTVLI 604
           DY+ +L+ DH     D S  IWT+L+
Sbjct: 595 DYLQELVRDHNNGNRDYSASIWTILM 620


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: 982
Number of extensions: 48
Number of successful extensions: 7
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: 635
Length adjustment: 38
Effective length of query: 594
Effective length of database: 597
Effective search space:   354618
Effective search space used:   354618
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 WP_027458901.1 K420_RS0115800 (XrtA/PEP-CTERM system amidotransferase)
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.3278619.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.6e-152  494.3   0.0     3e-152  494.1   0.0    1.0  1  NCBI__GCF_000519045.1:WP_027458901.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000519045.1:WP_027458901.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  494.1   0.0    3e-152    3e-152       1     517 []       2     561 ..       2     561 .. 0.92

  Alignments for each domain:
  == domain 1  score: 494.1 bits;  conditional E-value: 3e-152
                             TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlsegaQPlsnek.evv 72 
                                           Cgi+gi+d +   + +++ +++m+e++ hRGPD+ g++++    + +lghrRL+iidls+g+QPl+ne+ +v 
  NCBI__GCF_000519045.1:WP_027458901.1   2 CGITGIFDTRSRRDIDRAVLHRMNEAQFHRGPDEGGLHIE---PGLGLGHRRLSIIDLSTGQQPLYNEDkSVC 71 
                                           *********98877799********************999...7*************************999* PP

                             TIGR01536  73 ivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelflaRDrlGi 145
                                           +vfnGEIYN++eL  el++ G+ F+t+sDtEVi++a+e+wge++v+r++GmFAfalwd+++++lflaRDrlG+
  NCBI__GCF_000519045.1:WP_027458901.1  72 VVFNGEIYNYQELIPELQALGHVFHTRSDTEVIVHAWEAWGERCVDRFRGMFAFALWDRNRETLFLARDRLGV 144
                                           ************************************************************************* PP

                             TIGR01536 146 kPLYyase.qgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkelepakal.....dge 212
                                           kPL+ya   +g++lf+SE+K+lla+   k+ +d  a+ e+++l +v++++ +fk+ ++l+pa  l     ++ 
  NCBI__GCF_000519045.1:WP_027458901.1 145 KPLFYALLdDGSFLFGSELKSLLAHGGLKRDIDPCAVEEYFALGYVAEPRAIFKQARKLPPACTLllrrgQPV 217
                                           ******8779****************************************************99999988888 PP

                             TIGR01536 213 ekleeywevekee.vkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslvaaiakkeaksevktFs 284
                                            + +eyw+v+ +     s+ ++ +el + le+++k r++++vp+g++lSGG+DSs+v+a+++  ++++v+t s
  NCBI__GCF_000519045.1:WP_027458901.1 218 GQPREYWDVRFTLdNPISDADAQAELTHRLEESIKLRMISEVPLGAFLSGGVDSSAVVAMMAGLSANPVNTCS 290
                                           88888*****99866678899999************************************************* PP

                             TIGR01536 285 igfedskdldeskaarkvadelgtehkevliseeevlkeleevilaleeptairasiplyllsklarekgvkV 357
                                           igf  +++++es++ar vad   t+h+  ++++++ ++ ++ + +  +ep a++++ip+y +++lar++ v+V
  NCBI__GCF_000519045.1:WP_027458901.1 291 IGFS-DPAFNESEFARMVADRYHTNHHLDVVESDD-FDLIDTLARLYDEPYADSSAIPTYRVCQLARKH-VTV 360
                                           ****.**********************99988888.599******************************.*** PP

                             TIGR01536 358 vLsGeGaDElfgGYeyfreakaeeale................................lpeaselaekkl.. 396
                                           +LsG+G+DE fgGY +++   +ee+++                                +          +  
  NCBI__GCF_000519045.1:WP_027458901.1 361 ALSGDGGDESFGGYRRYKLHLMEEKMRsalplglrrplfgtlgklypkadwaprvfrakT----------Tfe 423
                                           ***************************9*9999999999999999888666333322220..........134 PP

                             TIGR01536 397 ..........llqaklakeselkellkakleeelkekeelkkelkee......seleellrldlelllsdllr 453
                                                     +++ ++ ++   ++l++ +++++l   ++l+  + ++        l+ +++ldl+++l ++++
  NCBI__GCF_000519045.1:WP_027458901.1 424 giarssvegyFHSVSILRAPMRNQLFSPQFKAALGGYDALQVFTDHAakadtqDPLALIQYLDLKTYLIGDIN 496
                                           55666667778888888888888888888887765544433322222234455999***************** PP

                             TIGR01536 454 ak.DrvsmahslEvRvPflDkelvelalsippelklrdgkeKvlLreaaeellPeeileRkKeaf 517
                                            k Dr+smahslEvR P++D++lve  +++p   k+r ++ K+lL++a+e +lP+++l+R+K++f
  NCBI__GCF_000519045.1:WP_027458901.1 497 TKvDRASMAHSLEVREPLMDHKLVEWLATLPSTQKIRGQEGKYLLKKAMEPHLPNDVLYRPKMGF 561
                                           ***************************************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (635 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: 22.49
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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