Alignments for a candidate for glnA in Mycolicibacterium vanbaalenii PYR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Mycolicibacterium vanbaalenii PYR-1

Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate WP_011780791.1 MVAN_RS18055 type I glutamate--ammonia ligase

Query= BRENDA::P64246
         (446 letters)



>NCBI__GCF_000015305.1:WP_011780791.1
          Length = 446

 Score =  814 bits (2102), Expect = 0.0
 Identities = 395/446 (88%), Positives = 417/446 (93%)

Query: 1   MDRQKEFVLRTLEERDIRFVRLWFTDVLGFLKSVAIAPAELEGAFEEGIGFDGSSIEGFA 60
           MDRQ EFVLRTLEERDIRFVRLWFTDVLG+LKSVAIAPAELEGAFEEGIGFDGSSIEGFA
Sbjct: 1   MDRQMEFVLRTLEERDIRFVRLWFTDVLGYLKSVAIAPAELEGAFEEGIGFDGSSIEGFA 60

Query: 61  RVSESDTVAHPDPSTFQVLPWATSSGHHHSARMFCDITMPDGSPSWADPRHVLRRQLTKA 120
           RVSE+D VA PDPSTFQVLPW TS+G+H+SARMFCDITMPDGSPSWAD RHVLRRQL+KA
Sbjct: 61  RVSEADMVARPDPSTFQVLPWTTSAGNHYSARMFCDITMPDGSPSWADSRHVLRRQLSKA 120

Query: 121 GELGFSCYVHPEIEFFLLKPGPEDGSVPVPVDNAGYFDQAVHDSALNFRRHAIDALEFMG 180
            +LGFSCYVHPEIEFFLLKPGP+DG+ P+P DN GYFDQAVHD+A NFRRHAIDALE MG
Sbjct: 121 SDLGFSCYVHPEIEFFLLKPGPDDGTQPIPADNGGYFDQAVHDAAPNFRRHAIDALEQMG 180

Query: 181 ISVEFSHHEGAPGQQEIDLRFADALSMADNVMTFRYVIKEVALEEGARASFMPKPFGQHP 240
           ISVEFSHHEGAPGQQEIDLR+ADALSMADNVMTFRY++KEVAL +G RASFMPKPF +HP
Sbjct: 181 ISVEFSHHEGAPGQQEIDLRYADALSMADNVMTFRYLVKEVALADGVRASFMPKPFAEHP 240

Query: 241 GSAMHTHMSLFEGDVNAFHSADDPLQLSEVGKSFIAGILEHACEISAVTNQWVNSYKRLV 300
           GSAMHTHMSLFEGD NAFHS DDPLQLS+VGKSFIAGILEHA EISAVTNQWVNSYKRLV
Sbjct: 241 GSAMHTHMSLFEGDTNAFHSPDDPLQLSDVGKSFIAGILEHANEISAVTNQWVNSYKRLV 300

Query: 301 QGGEAPTAASWGAANRSALVRVPMYTPHKTSSRRVEVRSPDSACNPYLTFAVLLAAGLRG 360
            GGEAPTAASWGAANRSALVRVPMYTPHK SSRRVEVRSPDSACNPYLTFAVLLAAGLRG
Sbjct: 301 HGGEAPTAASWGAANRSALVRVPMYTPHKVSSRRVEVRSPDSACNPYLTFAVLLAAGLRG 360

Query: 361 VEKGYVLGPQAEDNVWDLTPEERRAMGYRELPSSLDSALRAMEASELVAEALGEHVFDFF 420
           +EK YVLGPQAEDNVW LTPEERRAMGY+ELP SL  AL  ME SELVAEALGEHVFDFF
Sbjct: 361 IEKNYVLGPQAEDNVWSLTPEERRAMGYKELPGSLGVALTEMENSELVAEALGEHVFDFF 420

Query: 421 LRNKRTEWANYRSHVTPYELRTYLSL 446
           LRNKR+EW NYRSHVTP+EL+ YLSL
Sbjct: 421 LRNKRSEWENYRSHVTPFELKNYLSL 446


Lambda     K      H
   0.320    0.134    0.408 

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: 802
Number of extensions: 19
Number of successful extensions: 1
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: 446
Length of database: 446
Length adjustment: 32
Effective length of query: 414
Effective length of database: 414
Effective search space:   171396
Effective search space used:   171396
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 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate WP_011780791.1 MVAN_RS18055 (type I glutamate--ammonia ligase)
to HMM TIGR00653 (glnA: glutamine synthetase, type I (EC 6.3.1.2))

# 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/TIGR00653.hmm
# target sequence database:        /tmp/gapView.3370833.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00653  [M=462]
Accession:   TIGR00653
Description: GlnA: glutamine synthetase, type I
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.1e-140  452.9   0.0   1.9e-137  444.6   0.0    2.0  1  NCBI__GCF_000015305.1:WP_011780791.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000015305.1:WP_011780791.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  444.6   0.0  1.9e-137  1.9e-137       3     461 ..       8     444 ..       6     445 .. 0.97

  Alignments for each domain:
  == domain 1  score: 444.6 bits;  conditional E-value: 1.9e-137
                             TIGR00653   3 vlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkpdpetlviv 75 
                                           vl++l+e++++fv+l f+D+ G+lk+v+i   ele  a+eegi FDgss+eGf ++ e+D++  pdp+t++++
  NCBI__GCF_000015305.1:WP_011780791.1   8 VLRTLEERDIRFVRLWFTDVLGYLKSVAIAPAELE-GAFEEGIGFDGSSIEGFARVSEADMVARPDPSTFQVL 79 
                                           5678899***************************6.9************************************ PP

                             TIGR00653  76 Pfraek....vlrvicdvyepvtkepyerdpRsiakraeeelktklgdevyfGpEaEFflfdkvefkeasnss 144
                                           P++++     ++r++cd+  p ++ p+ +d R++++r + + + +lg + y+ pE+EFfl++    +      
  NCBI__GCF_000015305.1:WP_011780791.1  80 PWTTSAgnhySARMFCDITMP-DGSPSWADSRHVLRRQLSKAS-DLGFSCYVHPEIEFFLLKPGPDDG----- 145
                                           ***98788899*********9.*******************95.9****************9887773..... PP

                             TIGR00653 145 flevdseegewnreveegnkgykikkkggYfdvepvDkakdirrelvlaleelglevevsHHEvataqaEidi 217
                                                              ++  ++++ggYfd +  D a ++rr+ + ale++g++ve sHHE a++q+Eid+
  NCBI__GCF_000015305.1:WP_011780791.1 146 -------------------TQPIPADNGGYFDQAVHDAAPNFRRHAIDALEQMGISVEFSHHEGAPGQQEIDL 199
                                           ...................367899************************************************ PP

                             TIGR00653 218 kfdklvkaaDeivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdgenlfageegyagLsetal 290
                                           ++++++++aD++++++y vk va  +G  a+FmpKp+  ++gs mH+h+sl++   n+f+ +++  +Ls+ ++
  NCBI__GCF_000015305.1:WP_011780791.1 200 RYADALSMADNVMTFRYLVKEVALADGVRASFMPKPFAEHPGSAMHTHMSLFEGDTNAFHSPDDPLQLSDVGK 272
                                           ****************************************************************777****** PP

                             TIGR00653 291 yyigGilkHakalaAltnptvnsYkRLvpGyEAPvylaysaknRsaliRiPasa..npkakRiEvRspDpsan 361
                                            +i+Gil+Ha+ ++A+tn  vnsYkRLv G EAP   +++a nRsal+R+P+++  + +++R+EvRspD+++n
  NCBI__GCF_000015305.1:WP_011780791.1 273 SFIAGILEHANEISAVTNQWVNSYKRLVHGGEAPTAASWGAANRSALVRVPMYTphKVSSRRVEVRSPDSACN 345
                                           *****************************************************9878899************* PP

                             TIGR00653 362 pYLafaallmAgldGiknkidpgepldknlyelseeelkelGieqlpesLeealdelesdkevlkevlgeeli 434
                                           pYL+fa+ll+Agl Gi+++   g + + n+++l++ee++ +G ++lp sL  al e+e+  e++ e+lge+++
  NCBI__GCF_000015305.1:WP_011780791.1 346 PYLTFAVLLAAGLRGIEKNYVLGPQAEDNVWSLTPEERRAMGYKELPGSLGVALTEMENS-ELVAEALGEHVF 417
                                           **********************************************************99.9*********** PP

                             TIGR00653 435 eafielkrkEveelrlkvhpvElekyl 461
                                           + f+  kr+E+e++r +v+p+El++yl
  NCBI__GCF_000015305.1:WP_011780791.1 418 DFFLRNKRSEWENYRSHVTPFELKNYL 444
                                           *************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (462 nodes)
Target sequences:                          1  (446 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: 00:00:00.02
# Mc/sec: 9.41
//
[ok]

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