Alignments for a candidate for asnB in Rhodospirillum rubrum ATCC 11170

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Rhodospirillum rubrum ATCC 11170

Align asparagine synthase (glutamine-hydrolysing) 1; EC 6.3.5.4 (characterized)
to candidate YP_425322.1 Rru_A0230 asparagine synthase

Query= CharProtDB::CH_005185
         (632 letters)



>NCBI__GCF_000013085.1:YP_425322.1
          Length = 658

 Score =  297 bits (760), Expect = 1e-84
 Identities = 213/658 (32%), Positives = 329/658 (50%), Gaps = 61/658 (9%)

Query: 1   MCGFVGVFNKHPLAQ-TADQEELIKQMNQMIVHRGPDSDGYFHDEHVGF--GFRRLSIID 57
           MCG  G + +    +   +   L+ +M   + HRGPD DG + DE  G   G RRLSI+D
Sbjct: 1   MCGLTGYWTRGGDGRGRGEMTALVLRMAGALAHRGPDGDGAWVDEDAGLALGHRRLSIVD 60

Query: 58  VENGGQ-PLSYEDETYWIIFNGEIYNYIELREELEAKGYTFNTDSDTEVLLATYRHYKE- 115
           +   GQ P+   D    + +NGEIYN  ELR ELEA G  F   SDTEVLL  +  +   
Sbjct: 61  LSPAGQQPMVSADGRLALAYNGEIYNAAELRPELEAAGIVFRGHSDTEVLLEGFARWGVV 120

Query: 116 EAASKLRGMFAFLIWNKNDHVLYGARDPFGIKPLYYTTINDQVYFASERKSLMVAQN-DI 174
               +  GMFAF +W++ +  L   RD  GIKPLY       + FAS+ K +M   +   
Sbjct: 121 PTLRRAIGMFAFALWDRKERRLTLGRDRLGIKPLYVADHGGTLLFASQPKGMMPHPSWRG 180

Query: 175 EIDKEALQQYMSFQFVPEPSTLDAHVKKVEPGSQFTIRPDG-----------DITFKTYF 223
           E+D+E L   +    +P P ++   V ++ PG+      DG           ++  +   
Sbjct: 181 EVDREGLAAMLRLSCLPAPRSIFKGVSQLAPGTVVRFEADGRRSEEVFWSLEEVAARGVA 240

Query: 224 KANFKPVQTEEDKL-VKEVRDAIYDSVNVHMRSDVPVGSFLSGGIDSSFIVSVAKEFHPS 282
           +A  +P + E   L V+ +   + D+V   + +DVPVG+FLSGG+DSS +V++ ++    
Sbjct: 241 QARSQPARPESASLAVEHLESLLLDAVRRRLIADVPVGAFLSGGVDSSTVVALMRKVASG 300

Query: 283 -LKTFSVGFEQQGFSEVDVAKETAAALGIENISKVISPEEY---MNELPKIVWHFDDPLA 338
            +KTFS+GF ++G+ E   A   A  LG ++   V+SP+E    + +LP+  W +D+P A
Sbjct: 301 PVKTFSIGFAEEGWDESVHAAAVARHLGTDHRELVVSPDEVPAIVGDLPR--W-YDEPFA 357

Query: 339 DPAAIPLYFVAKEAKKHVTVALSGEGADELFGGYNIYREPLSLKPF-ERIPSGLKKMLLH 397
           D + IP   V+K A+  VTV+LSG+G DELF GYN + +   L    +RIP+  + +   
Sbjct: 358 DASQIPTLLVSKLARSEVTVSLSGDGGDELFAGYNRHVQGQRLWDLAQRIPTVGRDLGAA 417

Query: 398 VAAVMPEGM--RGKSLLERGCTPLQ--DRYIGNAKIFEESVKKQLLKHYNPNLSYRDVT- 452
           +      G   R   LL  G  P Q  D+    AKI       +LL+  +P   YR +  
Sbjct: 418 LIEAPSPGFWQRAVGLLPAGRRPPQAADK---PAKI------ARLLRARSPEALYRTLVG 468

Query: 453 -----------------KTYFTESSSYSD--INKMQYVDIHTWMRGDILLKADKMTMANS 493
                            + ++  S+   D  +++M+ +D   ++  DIL K D+ +MA  
Sbjct: 469 AMPSAEVPLAGVSLAAEERWYAASAEGVDSFVDRMRLLDAKGYLPDDILTKVDRASMAYG 528

Query: 494 LELRVPFLDKVVFDVASKIPDELKTKNGTTKYLLRKAAEGIVPEHVLNRKKLGFPVPIRH 553
           LE RVP LD  V + A  +P E+  + G  K+LLR+     VP  ++ R K+GF VP+  
Sbjct: 529 LEARVPLLDHRVVEFAWSLPPEMLIREGQGKWLLRRVLHRHVPRALIERPKMGFGVPLAA 588

Query: 554 WLKNEMNEWVRNII--QESQTDAYIHKDYVLQLLEDHCADKADNSRKIWTVLIFMIWH 609
           WL+  +  W  +++  Q       I    V +   DH A + D   ++W VL  + WH
Sbjct: 589 WLRGPLRGWAEDLLDPQTMAVQGLIDPAPVRRWWLDHLAGRRDTHDRLWPVLSALSWH 646


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: 952
Number of extensions: 51
Number of successful extensions: 9
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: 658
Length adjustment: 38
Effective length of query: 594
Effective length of database: 620
Effective search space:   368280
Effective search space used:   368280
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 YP_425322.1 Rru_A0230 (asparagine synthase)
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.21108.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                              -----------
     1e-146  475.8   0.0   1.2e-146  475.6   0.0    1.0  1  lcl|NCBI__GCF_000013085.1:YP_425322.1  Rru_A0230 asparagine synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000013085.1:YP_425322.1  Rru_A0230 asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  475.6   0.0  1.2e-146  1.2e-146       1     517 []       2     582 ..       2     582 .. 0.91

  Alignments for each domain:
  == domain 1  score: 475.6 bits;  conditional E-value: 1.2e-146
                              TIGR01536   1 Cgiagivdlkakake...eeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlseg.aQPlsne 68 
                                            Cg++g  ++  + +     ++ + +m+ +lahRGPD++g w d ++++ +lghrRL+i+dls + +QP+ ++
  lcl|NCBI__GCF_000013085.1:YP_425322.1   2 CGLTGYWTRGGDGRGrgeMTALVLRMAGALAHRGPDGDGAWVD-EDAGLALGHRRLSIVDLSPAgQQPMVSA 72 
                                            666665555444333344557899*******************.799***************998******* PP

                              TIGR01536  69 k.evvivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewg.eelverLeGmFAfalwdekkgelfl 138
                                            + + ++ +nGEIYN  eLr ele++G+ F+++sDtEV+L+ +  wg   ++ r  GmFAfalwd+k+++l l
  lcl|NCBI__GCF_000013085.1:YP_425322.1  73 DgRLALAYNGEIYNAAELRPELEAAGIVFRGHSDTEVLLEGFARWGvVPTLRRAIGMFAFALWDRKERRLTL 144
                                            *9********************************************************************** PP

                              TIGR01536 139 aRDrlGikPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkelepakal. 209
                                             RDrlGikPLY+a ++g+llfaS  K+++++++ + e+d+e+la +l l+  p ++++fk+v +l p+ ++ 
  lcl|NCBI__GCF_000013085.1:YP_425322.1 145 GRDRLGIKPLYVADHGGTLLFASQPKGMMPHPSWRGEVDREGLAAMLRLSCLPAPRSIFKGVSQLAPGTVVr 216
                                            **************************************************99*****************999 PP

                              TIGR01536 210 ...dgeekleeywevekee............vkeseeelveelrelledavkkrlvadvpvgvllSGGlDSs 266
                                               dg ++ e +w++e+ +            + es + +ve+l++ll dav++rl+advpvg++lSGG+DSs
  lcl|NCBI__GCF_000013085.1:YP_425322.1 217 feaDGRRSEEVFWSLEEVAargvaqarsqpaRPESASLAVEHLESLLLDAVRRRLIADVPVGAFLSGGVDSS 288
                                            97666666666****999999*****9999878889999********************************* PP

                              TIGR01536 267 lvaaiakkeaksevktFsigfedskdldeskaarkvadelgtehkevliseeevlkeleevilaleeptair 338
                                            +v+a+++k a ++vktFsigf+ ++  des +a++va++lgt+h+e+++s++ev + + ++ +  +ep+a++
  lcl|NCBI__GCF_000013085.1:YP_425322.1 289 TVVALMRKVASGPVKTFSIGFA-EEGWDESVHAAAVARHLGTDHRELVVSPDEVPAIVGDLPRWYDEPFADA 359
                                            **********************.************************************************* PP

                              TIGR01536 339 asiplyllsklarekgvkVvLsGeGaDElfgGYeyfreakaeeale.......................... 384
                                            ++ip++l+sklar + v+V LsG+G+DElf+GY+++ + ++  +l                           
  lcl|NCBI__GCF_000013085.1:YP_425322.1 360 SQIPTLLVSKLARSE-VTVSLSGDGGDELFAGYNRHVQGQRLWDLAqriptvgrdlgaalieapspgfwqra 430
                                            **************9.********************998666655578888888888888888888888888 PP

                              TIGR01536 385 .............lpeaselaekkl...............llqaklakeselkellkakleeelkekeelkk 428
                                                                                    +l+++l  ++ ++e+  a ++ + +e+   ++
  lcl|NCBI__GCF_000013085.1:YP_425322.1 431 vgllpagrrppqaA----------DkpakiarllrarspeALYRTLVGAMPSAEVPLAGVSLAAEERWYAAS 492
                                            88755544433330..........133444455566666678888889999999999999999999999998 PP

                              TIGR01536 429 elkeeseleellrldlelllsdllrak.DrvsmahslEvRvPflDkelvelalsippelklrdgkeKvlLre 499
                                            +   +s ++++  ld++ +l+d+++ k Dr+sma +lE+RvP+lD+++ve+a+s+ppe+ +r+g+ K+lLr+
  lcl|NCBI__GCF_000013085.1:YP_425322.1 493 AEGVDSFVDRMRLLDAKGYLPDDILTKvDRASMAYGLEARVPLLDHRVVEFAWSLPPEMLIREGQGKWLLRR 564
                                            99999******************************************************************* PP

                              TIGR01536 500 aaeellPeeileRkKeaf 517
                                            ++++++P+++ eR+K++f
  lcl|NCBI__GCF_000013085.1:YP_425322.1 565 VLHRHVPRALIERPKMGF 582
                                            ****************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (658 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: 00:00:00.02
# Mc/sec: 14.25
//
[ok]

This GapMind analysis is from Apr 10 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