Alignments for a candidate for asnB in Shewanella oneidensis MR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Shewanella oneidensis MR-1

Align asparagine synthase (glutamine-hydrolysing) 1; EC 6.3.5.4 (characterized)
to candidate 202285 SO3175 asparagine synthetase, glutamine-hydrolyzing (NCBI ptt file)

Query= CharProtDB::CH_005185
         (632 letters)



>FitnessBrowser__MR1:202285
          Length = 643

 Score =  315 bits (806), Expect = 5e-90
 Identities = 204/647 (31%), Positives = 348/647 (53%), Gaps = 47/647 (7%)

Query: 1   MCGFVGVFNKHPLAQTADQEELIKQMNQMIVHRGPDSDGYFH--DEHVGFGFRRLSIIDV 58
           MCGF G FN   L    D   +++ M   + +RGPDS G +   D+ +G   RRL+I+D+
Sbjct: 1   MCGFAGFFNTSNLT---DHARILECMGLELFNRGPDSFGIWFNSDDRIGLVHRRLAIVDL 57

Query: 59  ENGG-QPLSYEDETYWIIFNGEIYNYIELREELEA-KGYTFNTDSDTEVLLATYRHYKEE 116
              G QP++ +   Y I +NGEIYN+ ELR+ELE+ + Y +   SDTE LLA    +  +
Sbjct: 58  SAAGHQPMTSDSGRYIISYNGEIYNHQELRDELESIRQYNWRGHSDTETLLAAIEQWGLK 117

Query: 117 AA-SKLRGMFAFLIWNKNDHVLYGARDPFGIKPLYYTTINDQVYFASERKSLMVAQN-DI 174
               K  GMF   +W+  +  LY ARD FG KP+YY    D   FAS+  +     +   
Sbjct: 118 ITLQKATGMFGIALWDTLNKELYLARDRFGEKPVYYGLHKDAFIFASQLNAFRAYPDFKP 177

Query: 175 EIDKEALQQYMSFQFVPEPSTLDAHVKKVEPGSQFTIRPDGDITFKTYFKAN---FKPVQ 231
           EI+++++   +   ++P P ++ + + K+ P +   +  + +I+ +TY+ A         
Sbjct: 178 EINRDSITLLLRHNYIPAPYSIYSDIHKLLPATILKLDSNNNISLETYWSAKDIMSNASS 237

Query: 232 TEED----KLVKEVRDAIYDSVNVHMRSDVPVGSFLSGGIDSSFIVSVAK-EFHPSLKTF 286
           TE D    K V+ + + +  +V + M +DVP+G+FLSGG+DSS IVS+ + + +  +KTF
Sbjct: 238 TETDLPVGKQVEALENTLKKAVALQMSADVPLGAFLSGGVDSSLIVSLMQAQSNKPVKTF 297

Query: 287 SVGFEQQGFSEVDVAKETAAALGIENISKVISPEEYMNELPKIVWHFDDPLADPAAIPLY 346
           S+GF+   F+E   AKE A  LG E+    ++ E+ +  +PK+   +D+P +D + IP +
Sbjct: 298 SIGFDDPRFNEAVFAKEVAKHLGTEHTELYLTAEDALEVIPKLAEIYDEPFSDSSQIPTF 357

Query: 347 FVAKEAKKHVTVALSGEGADELFGGYNIYREPLSL-KPFERIPSGLKKMLLHVAAVMPE- 404
            V+K A+++VTV+LSG+  DELF GYN Y     + K    +P  L+  L +V   +P  
Sbjct: 358 LVSKIARQYVTVSLSGDAGDELFCGYNRYLMTSKVWKRLSVLPVFLRSFLANVFTFVPVN 417

Query: 405 --GMRGKSLLER-----------------GCTPLQDRYIGNAKIFEESVKKQLLKHYNPN 445
              + GK L  R                  C  ++  Y+G    + ++ ++ +L    P 
Sbjct: 418 VWNLFGKLLPSRLQLSNLGDKLHKAAAVLACRDVEQLYLGLVSHW-QNPEQVVLGSKEPL 476

Query: 446 LSYRDVTKTYFTESSSYSD-INKMQYVDIHTWMRGDILLKADKMTMANSLELRVPFLDKV 504
               D  +      +++SD I +M   D  +++  DIL+K D+  MA SLE RVPFLD  
Sbjct: 477 TVLTDPKR-----KANFSDPILQMMAQDTLSYLTDDILVKVDRAAMAVSLETRVPFLDHS 531

Query: 505 VFDVASKIPDELKTKNGTTKYLLRKAAEGIVPEHVLNRKKLGFPVPIRHWLKNEMNEWVR 564
           V + A ++  +LK ++G TK+ LR+     VP+ ++ R K+GF VP+  WL+  +  W  
Sbjct: 532 VLEHAWRLSLDLKLRDGKTKWCLREILYKYVPKDLIERPKMGFAVPLDAWLRGPLKVWAD 591

Query: 565 NII--QESQTDAYIHKDYVLQLLEDHCADKADNSRKIWTVLIFMIWH 609
           N++  +  + + +   + + ++ ++H + K +   ++W +L+F  W+
Sbjct: 592 NLLAAERLRQEGFFDAELIDRMWQEHKSGKRNWQYQLWDILMFQSWY 638


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: 1017
Number of extensions: 63
Number of successful extensions: 10
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: 643
Length adjustment: 38
Effective length of query: 594
Effective length of database: 605
Effective search space:   359370
Effective search space used:   359370
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 202285 SO3175 (asparagine synthetase, glutamine-hydrolyzing (NCBI ptt file))
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.29678.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-141  458.1   0.0   2.8e-141  457.9   0.0    1.0  1  lcl|FitnessBrowser__MR1:202285  SO3175 asparagine synthetase, gl


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:202285  SO3175 asparagine synthetase, glutamine-hydrolyzing (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  457.9   0.0  2.8e-141  2.8e-141       1     517 []       2     574 ..       2     574 .. 0.91

  Alignments for each domain:
  == domain 1  score: 457.9 bits;  conditional E-value: 2.8e-141
                       TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlseg.aQPlsnek.evvivfnG 77 
                                     Cg+ag+++ ++  +++ + ++ m   l  RGPD++g+w + ++++ +l+hrRLai+dls++ +QP+ +++ +++i +nG
  lcl|FitnessBrowser__MR1:202285   2 CGFAGFFNTSNL-TDHARILECMGLELFNRGPDSFGIWFN-SDDRIGLVHRRLAIVDLSAAgHQPMTSDSgRYIISYNG 78 
                                     ********9775.5556999999999**************.799***************999***************** PP

                       TIGR01536  78 EIYNheeLreelee.kGyeFetksDtEViLaayeewg.eelverLeGmFAfalwdekkgelflaRDrlGikPLYyaseq 154
                                     EIYNh+eLr+ele  + y+++++sDtE +Laa+e+wg + ++++ +GmF +alwd+ ++el+laRDr+G kP Yy+ ++
  lcl|FitnessBrowser__MR1:202285  79 EIYNHQELRDELESiRQYNWRGHSDTETLLAAIEQWGlKITLQKATGMFGIALWDTLNKELYLARDRFGEKPVYYGLHK 157
                                     ************97567************************************************************** PP

                       TIGR01536 155 gkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkelepakal....dgeekleeywevekee.... 225
                                     ++++faS + a+ a +++k+e++++ ++ ll +++ p + +++ ++++l pa  l    +++ +le+yw++++      
  lcl|FitnessBrowser__MR1:202285 158 DAFIFASQLNAFRAYPDFKPEINRDSITLLLRHNYIPAPYSIYSDIHKLLPATILkldsNNNISLETYWSAKDIMsnas 236
                                     *****************************************************99887767777788****99887776 PP

                       TIGR01536 226 ...vkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslvaaiakkeaksevktFsigfedskdldeskaark 301
                                        ++  + ++ve l+++l++av+ ++ advp+g++lSGG+DSsl++++++++++++vktFsigf+ ++ ++e+ +a++
  lcl|FitnessBrowser__MR1:202285 237 steTDLPVGKQVEALENTLKKAVALQMSADVPLGAFLSGGVDSSLIVSLMQAQSNKPVKTFSIGFD-DPRFNEAVFAKE 314
                                     644444456899******************************************************.************ PP

                       TIGR01536 302 vadelgtehkevliseeevlkeleevilaleeptairasiplyllsklarekgvkVvLsGeGaDElfgGYeyfreakae 380
                                     va++lgteh+e+++++e++l+ ++++  + +ep++++++ip++l+sk ar+  v+V LsG+ +DElf GY+++     +
  lcl|FitnessBrowser__MR1:202285 315 VAKHLGTEHTELYLTAEDALEVIPKLAEIYDEPFSDSSQIPTFLVSKIARQY-VTVSLSGDAGDELFCGYNRYLMT--S 390
                                     ***************************************************9.********************985..4 PP

                       TIGR01536 381 eale.....................................lpeaselaekkl...................llqakla 403
                                     + ++                                     l                               l+  l 
  lcl|FitnessBrowser__MR1:202285 391 KVWKrlsvlpvflrsflanvftfvpvnvwnlfgkllpsrlqL----------SnlgdklhkaaavlacrdveQLYLGLV 459
                                     444445698888888888888888888777777775554441..........022333334445567777677778888 PP

                       TIGR01536 404 keselkellkakleeelkekeelkkelkeeseleellrldlelllsdllrak.DrvsmahslEvRvPflDkelvelals 481
                                     +++++ e +   ++e l+  ++ k++ + +  + +++ +d+  +l+d++++k Dr++ma slE RvPflD+ ++e a++
  lcl|FitnessBrowser__MR1:202285 460 SHWQNPEQVVLGSKEPLTVLTDPKRKANFSDPILQMMAQDTLSYLTDDILVKvDRAAMAVSLETRVPFLDHSVLEHAWR 538
                                     999999999999999999999999999999************************************************* PP

                       TIGR01536 482 ippelklrdgkeKvlLreaaeellPeeileRkKeaf 517
                                     +  +lklrdgk+K+ Lre++ +++P+++ eR+K++f
  lcl|FitnessBrowser__MR1:202285 539 LSLDLKLRDGKTKWCLREILYKYVPKDLIERPKMGF 574
                                     **********************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (643 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: 9.84
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Downloads

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

Related tools

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