Alignments for a candidate for glnA in Desulfallas geothermicus DSM 3669

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Desulfallas geothermicus DSM 3669

Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate WP_092484472.1 BM299_RS11980 type I glutamate--ammonia ligase

Query= BRENDA::Q8PY99
         (447 letters)



>NCBI__GCF_900115975.1:WP_092484472.1
          Length = 439

 Score =  517 bits (1331), Expect = e-151
 Identities = 248/437 (56%), Positives = 315/437 (72%), Gaps = 5/437 (1%)

Query: 8   TTKEDVLEAVKERDVKFIRTQFTDTLGIIKSWAIPAEQLEEAFENGVMFDGSSIQGFTRI 67
           T+K+DV + VKE  ++FIR QFTD  GIIKS +I  ++L++AF   + FDGSSI GF RI
Sbjct: 5   TSKDDVYKLVKENGIEFIRLQFTDIFGIIKSTSIMVDELDKAFAGELFFDGSSIDGFARI 64

Query: 68  EESDMKLALDPSTFRILPWRPATGAVARILGDVYLPDGNPFKGDPRYVLKTAIKEAEKMG 127
           EESD  +  DPSTF+I+PWRP    VAR++ DVY PDG PF+G PRY+LK A++EAE+M 
Sbjct: 65  EESDQVIVPDPSTFKIMPWRPKEEGVARMICDVYAPDGKPFEGCPRYILKKAVREAEEMS 124

Query: 128 FSMNVGPELEFFLFKLDANGNPTTELTDQGGYFDFAPLDRAQDVRRDIDYALEHMGFQIE 187
           + +N+GPE EFFLF  D  G PT ++ D  GYFD AP+D  +D RR+I   L+ MGF+IE
Sbjct: 125 YKLNIGPEGEFFLFYTDEKGYPTFDIHDNAGYFDLAPVDMGEDARRNIILTLKKMGFKIE 184

Query: 188 ASHHEVAPSQHEIDFRFGDVLCTADNVVTFKYVVKSIAYHKGYYASFMPKPLFGVNGSGM 247
           ASHHEVAP QHEIDF++ + L TADN +TF+ VVK++A     YA+FMPKP  G NG+ M
Sbjct: 185 ASHHEVAPGQHEIDFKYDEALATADNWMTFRDVVKNVAKQFNLYATFMPKPFTGKNGNAM 244

Query: 248 HSNQSLFKDGKNVFYDPDTPTKLSQDAMYYIGGLLKHIREFTAVTNPVVNSYKRLVPGYE 307
           H NQSLF    +VFYD D    LS  A+ YIGGLLKH R    +TNP+VNSYKRL PGYE
Sbjct: 245 HCNQSLFSGDTDVFYDSDKADGLSDIALNYIGGLLKHARGMAPITNPIVNSYKRLKPGYE 304

Query: 308 APVYISWSAQNRSSLIRIPATRGNGTRIELRCPDPACNPYLAFALMLRAGLEGIKNKIDP 367
           AP++I+WS  NRS+LIRIPA RGN TR+ELR PDP  NPYL FA+MLRAGL+GIKN+I P
Sbjct: 305 APIHIAWSTSNRSTLIRIPAARGNSTRVELRNPDPTANPYLVFAVMLRAGLDGIKNEISP 364

Query: 368 GEPTNVNIFHLSDKEREERGIRSLPADLKEAIDEMKGSKFVKEALGEHVFSHYLCAKEME 427
             P N N++ + ++E     I   P DL+EAI EMK    ++E LG+H++  YL  K+ E
Sbjct: 365 PAPQNGNMYTMHNEE-----IPLFPRDLQEAIVEMKKDPLIRETLGDHIYERYLDVKQKE 419

Query: 428 WDEYKAVVHPWELSRYL 444
           W+EY   VH WE++RYL
Sbjct: 420 WNEYAETVHNWEINRYL 436


Lambda     K      H
   0.320    0.137    0.414 

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: 653
Number of extensions: 23
Number of successful extensions: 2
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: 447
Length of database: 439
Length adjustment: 32
Effective length of query: 415
Effective length of database: 407
Effective search space:   168905
Effective search space used:   168905
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_092484472.1 BM299_RS11980 (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.30722.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.2e-165  535.3   0.3   5.7e-163  528.8   0.3    2.0  1  lcl|NCBI__GCF_900115975.1:WP_092484472.1  BM299_RS11980 type I glutamate--


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900115975.1:WP_092484472.1  BM299_RS11980 type I glutamate--ammonia ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  528.8   0.3  5.7e-163  5.7e-163       2     461 ..       9     436 ..       8     437 .. 0.98

  Alignments for each domain:
  == domain 1  score: 528.8 bits;  conditional E-value: 5.7e-163
                                 TIGR00653   2 evlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkpdpe 70 
                                               +v kl+ke+ ++f++l+f+Di G++k+ +i v+el+ +a+   + FDgss+ Gf +ieesD +++pdp+
  lcl|NCBI__GCF_900115975.1:WP_092484472.1   9 DVYKLVKENGIEFIRLQFTDIFGIIKSTSIMVDELD-KAFAGELFFDGSSIDGFARIEESDQVIVPDPS 76 
                                               6889*******************************8.9999**************************** PP

                                 TIGR00653  71 tlvivPfraek..vlrvicdvyepvtkepyerdpRsiakraeeelktklgdevyfGpEaEFflfdkvef 137
                                               t++i+P+r ++  v+r+icdvy p +++p+e++pR+i+k+a  e  +++++++++GpE EFflf ++e+
  lcl|NCBI__GCF_900115975.1:WP_092484472.1  77 TFKIMPWRPKEegVARMICDVYAP-DGKPFEGCPRYILKKAVREA-EEMSYKLNIGPEGEFFLFYTDEK 143
                                               ********98889***********.*******************9.5******************9999 PP

                                 TIGR00653 138 keasnssflevdseegewnreveegnkgykikkkggYfdvepvDkakdirrelvlaleelglevevsHH 206
                                               +                          ++ i+++ gYfd++pvD  +d rr+++l+l+++g+++e+sHH
  lcl|NCBI__GCF_900115975.1:WP_092484472.1 144 GYP------------------------TFDIHDNAGYFDLAPVDMGEDARRNIILTLKKMGFKIEASHH 188
                                               844........................7899************************************** PP

                                 TIGR00653 207 EvataqaEidikfdklvkaaDeivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdgenl 275
                                               Eva++q+Eid+k+d+++ +aD+ ++++ vvknvak+  ++atFmpKp++g+ng+ mH+++sl++   ++
  lcl|NCBI__GCF_900115975.1:WP_092484472.1 189 EVAPGQHEIDFKYDEALATADNWMTFRDVVKNVAKQFNLYATFMPKPFTGKNGNAMHCNQSLFSGDTDV 257
                                               ********************************************************************* PP

                                 TIGR00653 276 fageegyagLsetalyyigGilkHakalaAltnptvnsYkRLvpGyEAPvylaysaknRsaliRiPasa 344
                                               f+++++  gLs+ al yigG+lkHa+++a +tnp vnsYkRL pGyEAP+ +a+s++nRs+liRiPa++
  lcl|NCBI__GCF_900115975.1:WP_092484472.1 258 FYDSDKADGLSDIALNYIGGLLKHARGMAPITNPIVNSYKRLKPGYEAPIHIAWSTSNRSTLIRIPAAR 326
                                               ********************************************************************* PP

                                 TIGR00653 345 npkakRiEvRspDpsanpYLafaallmAgldGiknkidpgepldknlyelseeelkelGieqlpesLee 413
                                                ++++R+E+R pDp+anpYL fa++l AgldGikn+i p++p + n+y + +ee     i+  p++L+e
  lcl|NCBI__GCF_900115975.1:WP_092484472.1 327 -GNSTRVELRNPDPTANPYLVFAVMLRAGLDGIKNEISPPAPQNGNMYTMHNEE-----IPLFPRDLQE 389
                                               .*************************************************9886.....788******* PP

                                 TIGR00653 414 aldelesdkevlkevlgeelieafielkrkEveelrlkvhpvElekyl 461
                                               a+ e+++d  +++e lg++++e+++++k+kE++e+  +vh++E+++yl
  lcl|NCBI__GCF_900115975.1:WP_092484472.1 390 AIVEMKKD-PLIRETLGDHIYERYLDVKQKEWNEYAETVHNWEINRYL 436
                                               ********.99***********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (462 nodes)
Target sequences:                          1  (439 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: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 4.55
//
[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