Alignments for a candidate for glnA in Persephonella marina EX-H1

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Persephonella marina EX-H1

Align glutamine synthetase, type I (characterized)
to candidate WP_012676471.1 PERMA_RS07870 type I glutamate--ammonia ligase

Query= metacyc::SYNPCC7942_2156-MONOMER
         (473 letters)



>NCBI__GCF_000021565.1:WP_012676471.1
          Length = 475

 Score =  593 bits (1529), Expect = e-174
 Identities = 281/470 (59%), Positives = 353/470 (75%), Gaps = 2/470 (0%)

Query: 3   ETAQEVLQLIQEKGIQLVDLKFIDMPGIWQHLTLHVSQIDENSFVEGVPFDGSSIRGWKA 62
           +T  +VL++I EKGI  +DLKF D  G WQHLT+   +    SF  G+PFDGSSIRGWK 
Sbjct: 7   QTPDDVLRVISEKGIVFIDLKFSDPFGQWQHLTIPAHEFSAESFENGIPFDGSSIRGWKG 66

Query: 63  INESDMTMVPDPTTAWIDPFMKEPTLSMICTIYEPRTNTPYERCPRAIAQKAVDYLKASG 122
           I ESDM ++PDP +A+IDPF++EPT+S++C + +P T   Y R PR IA+KA+++LK++G
Sbjct: 67  IQESDMLLIPDPKSAFIDPFIEEPTISLVCDVEDPITREAYNRDPRQIAKKAIEFLKSTG 126

Query: 123 IGDTAYFGPEAEFFIFDDVRFDQAENKSYYYVDSIEGRWNSGREEEGGNLGYKPRYKEGY 182
           IGD A+FGPEAEFFIFDD++F    N SYY +DS+EG WN+GREE   NLGYK  YK GY
Sbjct: 127 IGDIAFFGPEAEFFIFDDIKFSNGPNHSYYEIDSVEGWWNTGREEMP-NLGYKTPYKRGY 185

Query: 183 FPVAPTDTSQDMRSEMLLTMADCGVPIEKHHHEVATGGQCELGFRFGKLIEAADWLMTYK 242
           FPV P D    +R +M+ T+ + G+ +E+ HHEV T GQ E+ FRF  L+   D ++ YK
Sbjct: 186 FPVPPLDKMSAIRRDMVKTLEEVGITVEREHHEVGTAGQGEINFRFADLVTTGDNVLKYK 245

Query: 243 YVIKNVGRRYGKTITFMPKPLFNDNGSGMHTHQSIWNDGQPLFAGDQYAGLSQMALWYIG 302
           YV++NVG ++GK +TF+PKP+  DNG+GMH H SIW  G+ +FAGDQYAGLS++AL+ IG
Sbjct: 246 YVLRNVGFKHGKYVTFLPKPIAGDNGTGMHIHFSIWKGGENMFAGDQYAGLSEIALYAIG 305

Query: 303 GILKHAPALLALTNPTTNSYKRLVPGFEAPVNLAYSQGNRSASVRIPLSGTNPKAKRLEF 362
           GI+KH  A+ A TNPTTNSY RLVPGFEAPV LAYS  NRSA++RIP+   +PKAKR+E 
Sbjct: 306 GIIKHGKAIAAFTNPTTNSYHRLVPGFEAPVRLAYSARNRSAAIRIPMGSASPKAKRIEV 365

Query: 363 RCPDATSNPYLAFAAMLCAGIDGIKNQIDPGEPLDVDIYDLSPEELAKIPSTPGSLKDAL 422
           R PDA+SNPYLAF A+L A IDGI+N+I PGEPLD DIY LSPEELA +P TP SL++A+
Sbjct: 366 RFPDASSNPYLAFVALLMAAIDGIENKIHPGEPLDKDIYSLSPEELANVPETPASLQEAI 425

Query: 423 KALEADHDFLTVGGVFTEDFIQNWIEYKLDNEVIPISLRPHPYEFALYYD 472
            AL+AD DFL  GGV  EDFIQ WIE K   EV  I L PHP EF LYYD
Sbjct: 426 DALKADMDFLLKGGVMDEDFIQMWIETK-QEEVDAIRLVPHPKEFELYYD 474


Lambda     K      H
   0.319    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: 748
Number of extensions: 33
Number of successful extensions: 3
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: 473
Length of database: 475
Length adjustment: 33
Effective length of query: 440
Effective length of database: 442
Effective search space:   194480
Effective search space used:   194480
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: 51 (24.3 bits)

Align candidate WP_012676471.1 PERMA_RS07870 (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.25356.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     1e-202  659.8   0.0   1.2e-202  659.6   0.0    1.0  1  lcl|NCBI__GCF_000021565.1:WP_012676471.1  PERMA_RS07870 type I glutamate--


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000021565.1:WP_012676471.1  PERMA_RS07870 type I glutamate--ammonia ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  659.6   0.0  1.2e-202  1.2e-202       2     462 .]      11     474 ..      10     474 .. 0.98

  Alignments for each domain:
  == domain 1  score: 659.6 bits;  conditional E-value: 1.2e-202
                                 TIGR00653   2 evlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkpdpe 70 
                                               +vl+++ e+ + f+dl+f+D  G++++++ip++e+++e +e+gi FDgss++G+k+i+esD+ll pdp+
  lcl|NCBI__GCF_000021565.1:WP_012676471.1  11 DVLRVISEKGIVFIDLKFSDPFGQWQHLTIPAHEFSAESFENGIPFDGSSIRGWKGIQESDMLLIPDPK 79 
                                               678899*************************************************************** PP

                                 TIGR00653  71 tlvivPfraekvlrvicdvyepvtkepyerdpRsiakraeeelk.tklgdevyfGpEaEFflfdkvefk 138
                                               +++i+Pf++e++++++cdv +p+t+e y+rdpR+iak+a e lk t++gd ++fGpEaEFf+fd+++f+
  lcl|NCBI__GCF_000021565.1:WP_012676471.1  80 SAFIDPFIEEPTISLVCDVEDPITREAYNRDPRQIAKKAIEFLKsTGIGDIAFFGPEAEFFIFDDIKFS 148
                                               ********************************************************************* PP

                                 TIGR00653 139 easnssflevdseegewn.reveegnkgykikkkggYfdvepvDkakdirrelvlaleelglevevsHH 206
                                               +  n+s++e+ds+eg+wn  ++e  n gyk+  k+gYf+v+p+Dk+  irr++v++lee+g++ve +HH
  lcl|NCBI__GCF_000021565.1:WP_012676471.1 149 NGPNHSYYEIDSVEGWWNtGREEMPNLGYKTPYKRGYFPVPPLDKMSAIRRDMVKTLEEVGITVEREHH 217
                                               ******************5555666******************************************** PP

                                 TIGR00653 207 Evata.qaEidikfdklvkaaDeivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdgen 274
                                               Ev+ta q Ei+++f++lv+++D++++yKyv +nv  khGk++tF+pKp+ gdng GmH+h+s+wk gen
  lcl|NCBI__GCF_000021565.1:WP_012676471.1 218 EVGTAgQGEINFRFADLVTTGDNVLKYKYVLRNVGFKHGKYVTFLPKPIAGDNGTGMHIHFSIWKGGEN 286
                                               ********************************************************************* PP

                                 TIGR00653 275 lfageegyagLsetalyyigGilkHakalaAltnptvnsYkRLvpGyEAPvylaysaknRsaliRiPas 343
                                               +fag++ yagLse aly igGi+kH+ka+aA+tnpt+nsY+RLvpG+EAPv laysa+nRsa+iRiP+ 
  lcl|NCBI__GCF_000021565.1:WP_012676471.1 287 MFAGDQ-YAGLSEIALYAIGGIIKHGKAIAAFTNPTTNSYHRLVPGFEAPVRLAYSARNRSAAIRIPMG 354
                                               ******.*************************************************************9 PP

                                 TIGR00653 344 a.npkakRiEvRspDpsanpYLafaallmAgldGiknkidpgepldknlyelseeelkelGieqlpesL 411
                                               + +pkakRiEvR+pD+s+npYLaf allmA++dGi+nki+pgepldk++y+ls+eel++  ++++p+sL
  lcl|NCBI__GCF_000021565.1:WP_012676471.1 355 SaSPKAKRIEVRFPDASSNPYLAFVALLMAAIDGIENKIHPGEPLDKDIYSLSPEELAN--VPETPASL 421
                                               99*********************************************************..******** PP

                                 TIGR00653 412 eealdelesdk..evlkevlgeelieafielkrkEveelrlkvhpvElekyld 462
                                               +ea+d+l++d   +++++v+ e++i+ +ie+k++Ev+ +rl +hp E+e y+d
  lcl|NCBI__GCF_000021565.1:WP_012676471.1 422 QEAIDALKADMdfLLKGGVMDEDFIQMWIETKQEEVDAIRLVPHPKEFELYYD 474
                                               **********988999***********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (462 nodes)
Target sequences:                          1  (475 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: 8.45
//
[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