Alignments for a candidate for asnB in Mesorhizobium ciceri WSM1271

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Mesorhizobium ciceri WSM1271

Align Putative asparagine synthetase [glutamine-hydrolyzing]; EC 6.3.5.4 (characterized)
to candidate YP_004144523.1 Mesci_5375 asparagine synthase

Query= SwissProt::P64248
         (652 letters)



>NCBI__GCF_000185905.1:YP_004144523.1
          Length = 673

 Score =  243 bits (620), Expect = 2e-68
 Identities = 202/613 (32%), Positives = 292/613 (47%), Gaps = 80/613 (13%)

Query: 1   MCGLLAFVAAPAGAAGPEGADAASAIARASHLMRHRGPDESGTWHAVDGASGGVVFGFNR 60
           MCG+   VA  A A  P  A    A+ R +  + HRGPDESG +   D  +G       R
Sbjct: 1   MCGIAGIVALNAAAEPPSRA----ALLRMAAALSHRGPDESGVYR--DRRAG---LAHTR 51

Query: 61  LSIIDIAHSHQPLRWGPPEAPDRYVLVFNGEIYNYLELRDELRTQHGAVFATDGDGEAIL 120
           LS+ID++   QPL     +  D   +VFNGEI+NY+ELR++L    G  F T  D E I+
Sbjct: 52  LSVIDLSTGQQPLA----DTGDTTWIVFNGEIFNYVELREQLMAL-GHRFRTRSDTEVIV 106

Query: 121 AGYHHWGTEVLQRLRGMFAFALWDTVTRELFCARDPFGIKPLFIATGAGGTAVASEKKCL 180
             Y  WG    +RL G +A A+WD++T  L  +RD FGI PL +   AG    ASE K +
Sbjct: 107 HAYRAWGVAAFERLNGQWALAIWDSLTGRLVLSRDRFGICPLHLCEHAGRLHFASEVKAI 166

Query: 181 LDLVELV--GFD-TEIDHRALQHYTVLQYVPEPETLHRGVRRLESGCFARIRADQLAPVI 237
                 +   FD   ID    Q +T+   VP P+ + +GV+ L  G    +R      V 
Sbjct: 167 FAADPAIPRAFDPAGID----QTFTLWTVVP-PQGVFQGVKELTPG---HVRIYDNGSVR 218

Query: 238 TRYF-------VPRFAASPITNDNDQARYDEITAVLEDSVAKHM-RADVTVGAFLSGGID 289
              F       +   A    T   D A  DE+ + L+ + A  M +ADV VG +LSGG+D
Sbjct: 219 EHAFWKPCYPEIADQAHGTFTGSLDDA-VDEVRSALQAATALRMVKADVPVGCYLSGGLD 277

Query: 290 STAIAALAIRH-NPRLITFTTGFEREGFSEIDVAVASAEAIGARHIAKVVSADEFVAALP 348
           S+ +A L  R       TF+  F    + E       A A G  H   +VS  +     P
Sbjct: 278 SSLVAMLGRRFAGAPFQTFSLRFADAEYDETRYQRLVASASGGEHHEVMVSRGDIAEVFP 337

Query: 349 EIVWYLDEPVADPALVPLFFVAREARKH-VKVVLSGEGADELFGGYTIYREPLSLRPFDY 407
           +++ + + P+   A  PLF ++R  R+H +KVVL+GEGADE+F GY ++RE         
Sbjct: 338 DVIRHAERPILRTAPAPLFLLSRLVREHGIKVVLTGEGADEMFAGYDLFRE--------- 388

Query: 408 LPKPLRRSMGKVSKPLPEGMRGKSLLHRGSLTLEE---RYYGNARSFSGAQLREV-LPGF 463
               +RR  G+     P   R   LL R    L     +    AR F G  +     PGF
Sbjct: 389 --GKVRRFWGR----QPASARRARLLERLYPYLSRSPVKQQAMARQFFGLGIHAFGAPGF 442

Query: 464 RPD--WTHTDV-----TAPVYAESA-----------------GWDPVARMQHIDLFTWLR 499
             D  W  T       +A ++AE+A                  W P+A+ Q++++ T + 
Sbjct: 443 AHDTRWRTTSAIKRLFSAGMHAEAARHDVVADLLGRLPEEFPRWGPLAQDQYLEIRTLMS 502

Query: 500 GDIL-VKADKITMANSLELRVPFLDPEVFAVASRLPAGAKITRTTTKYALRRALEPIVPA 558
           G +L  + D++ MA+S+E R PFLD  + A+A+ LP   K+     K+ L+R  + IVPA
Sbjct: 503 GYLLSSQGDRMLMAHSVEGRFPFLDDRLVALANSLPPDYKLRILDEKHVLKRVAKSIVPA 562

Query: 559 HVLHRPKLGFPVP 571
            V+ R K  +  P
Sbjct: 563 EVVARKKQPYRAP 575


Lambda     K      H
   0.323    0.138    0.428 

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: 1065
Number of extensions: 50
Number of successful extensions: 8
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: 652
Length of database: 673
Length adjustment: 38
Effective length of query: 614
Effective length of database: 635
Effective search space:   389890
Effective search space used:   389890
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 54 (25.4 bits)

Align candidate YP_004144523.1 Mesci_5375 (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.7728.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.3e-171  558.0   0.0   1.5e-171  557.8   0.0    1.0  1  lcl|NCBI__GCF_000185905.1:YP_004144523.1  Mesci_5375 asparagine synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000185905.1:YP_004144523.1  Mesci_5375 asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  557.8   0.0  1.5e-171  1.5e-171       1     517 []       2     572 ..       2     572 .. 0.96

  Alignments for each domain:
  == domain 1  score: 557.8 bits;  conditional E-value: 1.5e-171
                                 TIGR01536   1 Cgiagivdlkakake.eeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlsegaQPlsne 68 
                                               Cgiagiv+l+a+a+  +++a+ +m+ +l+hRGPD++gv++d    +a+l+h RL++idls+g+QPl+++
  lcl|NCBI__GCF_000185905.1:YP_004144523.1   2 CGIAGIVALNAAAEPpSRAALLRMAAALSHRGPDESGVYRD---RRAGLAHTRLSVIDLSTGQQPLADT 67 
                                               ***********9999*99***********************...7************************ PP

                                 TIGR01536  69 k.evvivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgel 136
                                               + +++ivfnGEI+N+ eLre+l + G++F+t+sDtEVi++ay++wg +++erL+G++A+a+wd+ +g+l
  lcl|NCBI__GCF_000185905.1:YP_004144523.1  68 GdTTWIVFNGEIFNYVELREQLMALGHRFRTRSDTEVIVHAYRAWGVAAFERLNGQWALAIWDSLTGRL 136
                                               **99***************************************************************** PP

                                 TIGR01536 137 flaRDrlGikPLYyaseqgkllfaSEiKallalk.eikaeldkealaelltlqlvptektlfkevkele 204
                                               +l+RDr+Gi+PL+ ++++g+l+faSE+Ka++a++ +i++++d +++ +++tl++v++++ +f++vkel+
  lcl|NCBI__GCF_000185905.1:YP_004144523.1 137 VLSRDRFGICPLHLCEHAGRLHFASEVKAIFAADpAIPRAFDPAGIDQTFTLWTVVPPQGVFQGVKELT 205
                                               **********************************9********************************** PP

                                 TIGR01536 205 pakal..dgeeklee.ywevekee........vkeseeelveelrelledavkkrlv.advpvgvllSG 261
                                               p++++  d+   +e+ +w+  ++e        ++ s++++v+e+r++l++a++ r+v advpvg++lSG
  lcl|NCBI__GCF_000185905.1:YP_004144523.1 206 PGHVRiyDNGSVREHaFWKPCYPEiadqahgtFTGSLDDAVDEVRSALQAATALRMVkADVPVGCYLSG 274
                                               *****97554555557999999999999999999**********************99*********** PP

                                 TIGR01536 262 GlDSslvaaiakkeaksevktFsigfedskdldeskaarkvadelgtehkevliseeevlkeleevila 330
                                               GlDSslva++ +++a ++++tFs++f+ ++++de++++r va + g eh+ev++s+ ++++ +++vi++
  lcl|NCBI__GCF_000185905.1:YP_004144523.1 275 GLDSSLVAMLGRRFAGAPFQTFSLRFA-DAEYDETRYQRLVASASGGEHHEVMVSRGDIAEVFPDVIRH 342
                                               ***************************.***************************************** PP

                                 TIGR01536 331 leeptairasiplyllsklarekgvkVvLsGeGaDElfgGYeyfreakaeeale............... 384
                                                e+p+  +a +pl+lls+l+re+g+kVvL+GeGaDE+f+GY+ fre k+++ +                
  lcl|NCBI__GCF_000185905.1:YP_004144523.1 343 AERPILRTAPAPLFLLSRLVREHGIKVVLTGEGADEMFAGYDLFREGKVRRFWGrqpasarrarllerl 411
                                               *****************************************************9999999999998888 PP

                                 TIGR01536 385 lpease..laekkl.................llqaklakeselkellkakleeelkekeelkkelkee. 433
                                               +p++s+  ++++++                 +++++++++s+ k+l++a +++e ++++ +++ l +  
  lcl|NCBI__GCF_000185905.1:YP_004144523.1 412 YPYLSRspVKQQAMarqffglgihafgapgfAHDTRWRTTSAIKRLFSAGMHAEAARHDVVADLLGRLp 480
                                               66665554333333666789999*******9**************************999999888888 PP

                                 TIGR01536 434 ......seleellrldlelllsdllrak..DrvsmahslEvRvPflDkelvelalsippelklrdgkeK 494
                                                       l++ ++l++ +l+s++l+ +  Dr++mahs+E R+PflD++lv la s+pp++klr  +eK
  lcl|NCBI__GCF_000185905.1:YP_004144523.1 481 eefprwGPLAQDQYLEIRTLMSGYLLSSqgDRMLMAHSVEGRFPFLDDRLVALANSLPPDYKLRILDEK 549
                                               8899999******************9999**************************************** PP

                                 TIGR01536 495 vlLreaaeellPeeileRkKeaf 517
                                               ++L+++a++++P e++ RkK+++
  lcl|NCBI__GCF_000185905.1:YP_004144523.1 550 HVLKRVAKSIVPAEVVARKKQPY 572
                                               *********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (673 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: 9.64
//
[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