Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate WP_029329000.1 ON01_RS05550 type I glutamate--ammonia ligase
Query= BRENDA::P12425 (444 letters) >NCBI__GCF_000224785.1:WP_029329000.1 Length = 445 Score = 731 bits (1886), Expect = 0.0 Identities = 344/439 (78%), Positives = 393/439 (89%) Query: 6 REDIEKLVKEENVKYIRLQFTDILGTIKNVEIPVSQLGKALDNKVMFDGSSIEGFVRIEE 65 ++DI K++ EE+V++IRLQFTD+LGTIKNVEIP SQL KA DNK+MFDGSSIEGFVRI+E Sbjct: 7 KQDIYKMIDEESVRFIRLQFTDMLGTIKNVEIPYSQLEKAFDNKMMFDGSSIEGFVRIDE 66 Query: 66 SDMYLYPDLNTFVIFPWTAEKGKVARFICDIYNPDGTPFEGDPRNNLKRILKEMEDLGFS 125 SDMYLYPDL+TFV+FPWTAEKGKVARFICDIYNPDGTPFEG PR NLKR LK ME+LG+S Sbjct: 67 SDMYLYPDLDTFVVFPWTAEKGKVARFICDIYNPDGTPFEGCPRYNLKRNLKRMEELGYS 126 Query: 126 DFNLGPEPEFFLFKLDEKGEPTLELNDKGGYFDLAPTDLGENCRRDIVLELEEMGFEIEA 185 FN+G EPEFFLFKLDEKG+P +ELND+GGYFDLAPTDLGENCRRDIVLELEEMGFEIEA Sbjct: 127 AFNIGTEPEFFLFKLDEKGDPMMELNDRGGYFDLAPTDLGENCRRDIVLELEEMGFEIEA 186 Query: 186 SHHEVAPGQHEIDFKYAGAVRSCDDIQTFKLVVKTIARKHGLHATFMPKPLFGVNGSGMH 245 SHHEVAPGQHEIDFKY+ AV+ DDIQTFKLVVKTIARKH LHATFMPKPLFGVNGSGMH Sbjct: 187 SHHEVAPGQHEIDFKYSDAVKHADDIQTFKLVVKTIARKHNLHATFMPKPLFGVNGSGMH 246 Query: 246 CNLSLFKNGVNAFFDENADLQLSETAKHFIAGIVKHATSFTAVTNPTVNSYKRLVPGYEA 305 N+SLFK+G N F+DE D+Q+S T K F AGI+KHAT+FTAVTNPTVNSYKRLVPGYEA Sbjct: 247 VNMSLFKDGRNVFYDEKGDMQVSTTLKQFTAGIIKHATNFTAVTNPTVNSYKRLVPGYEA 306 Query: 306 PCYVAWSAQNRSPLIRIPASRGISTRVEVRSVDPAANPYLALSVLLAAGLDGIKNKLEAP 365 PCYVAWS NRSPL+R+P+SRG+STR+E RSVDPAANPY+ L+VLL+AGLDGI+NKL P Sbjct: 307 PCYVAWSGLNRSPLVRVPSSRGLSTRIEARSVDPAANPYMTLAVLLSAGLDGIENKLTPP 366 Query: 366 APIDRNIYVMSKEERMENGIVDLPATLAEALEEFKSNEVMVKALGEHLFEHFIEAKEIEW 425 P+D+NIY M K ER E+GI LPATL +ALEE ++ V+ +ALG HL+EHF+EAK+IEW Sbjct: 367 EPVDQNIYEMDKAEREEHGIKSLPATLMDALEELDNDPVITEALGNHLYEHFVEAKQIEW 426 Query: 426 DMFRTQVHPWEREQYMSQY 444 DMFRT VHPWEREQY++ Y Sbjct: 427 DMFRTAVHPWEREQYLTSY 445 Lambda K H 0.319 0.137 0.406 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: 727 Number of extensions: 24 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: 444 Length of database: 445 Length adjustment: 32 Effective length of query: 412 Effective length of database: 413 Effective search space: 170156 Effective search space used: 170156 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_029329000.1 ON01_RS05550 (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.2750803.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.4e-185 601.4 0.2 4.8e-183 595.0 0.2 2.0 1 NCBI__GCF_000224785.1:WP_029329000.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000224785.1:WP_029329000.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 595.0 0.2 4.8e-183 4.8e-183 2 461 .. 9 442 .. 8 443 .. 0.98 Alignments for each domain: == domain 1 score: 595.0 bits; conditional E-value: 4.8e-183 TIGR00653 2 evlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkpdpetlvi 74 ++ k+++ee v+f++l+f+D+ G++k+veip+s+le +a++++++FDgss+eGf++i+esD++l+pd++t+v+ NCBI__GCF_000224785.1:WP_029329000.1 9 DIYKMIDEESVRFIRLQFTDMLGTIKNVEIPYSQLE-KAFDNKMMFDGSSIEGFVRIDESDMYLYPDLDTFVV 80 6889*******************************6.9*********************************** PP TIGR00653 75 vPfraek..vlrvicdvyepvtkepyerdpRsiakraeeelktklgdevyfGpEaEFflfdkvefkeasnssf 145 +P++aek v+r+icd+y+p +++p+e++pR+++kr ++++++ + +++G+E+EFflf+ +e+++ NCBI__GCF_000224785.1:WP_029329000.1 81 FPWTAEKgkVARFICDIYNP-DGTPFEGCPRYNLKRNLKRMEELGYSAFNIGTEPEFFLFKLDEKGDP----- 147 *****9999***********.********************876677789***********9999855..... PP TIGR00653 146 levdseegewnreveegnkgykikkkggYfdvepvDkakdirrelvlaleelglevevsHHEvataqaEidik 218 ++++++ggYfd++p+D +++rr++vl+lee+g+e+e+sHHEva++q+Eid+k NCBI__GCF_000224785.1:WP_029329000.1 148 -------------------MMELNDRGGYFDLAPTDLGENCRRDIVLELEEMGFEIEASHHEVAPGQHEIDFK 201 ...................67899************************************************* PP TIGR00653 219 fdklvkaaDeivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdgenlfageegyagLsetaly 291 ++++vk+aD+i+++K+vvk++a+kh ++atFmpKplfg ngsGmHv++sl+kdg+n+f++e+g++++s t + NCBI__GCF_000224785.1:WP_029329000.1 202 YSDAVKHADDIQTFKLVVKTIARKHNLHATFMPKPLFGVNGSGMHVNMSLFKDGRNVFYDEKGDMQVSTTLKQ 274 ***************************************************************999******* PP TIGR00653 292 yigGilkHakalaAltnptvnsYkRLvpGyEAPvylaysaknRsaliRiPasanpkakRiEvRspDpsanpYL 364 + +Gi+kHa+ ++A+tnptvnsYkRLvpGyEAP+y+a+s nRs+l+R+P s+ + ++RiE Rs+Dp+anpY+ NCBI__GCF_000224785.1:WP_029329000.1 275 FTAGIIKHATNFTAVTNPTVNSYKRLVPGYEAPCYVAWSGLNRSPLVRVPSSR-GLSTRIEARSVDPAANPYM 346 ****************************************************9.******************* PP TIGR00653 365 afaallmAgldGiknkidpgepldknlyelseeelkelGieqlpesLeealdelesdkevlkevlgeelieaf 437 ++a+ll AgldGi+nk++p+ep+d+n+ye++++e++e+Gi++lp++L +al+el++d v++e+lg++l+e+f NCBI__GCF_000224785.1:WP_029329000.1 347 TLAVLLSAGLDGIENKLTPPEPVDQNIYEMDKAEREEHGIKSLPATLMDALEELDND-PVITEALGNHLYEHF 418 *********************************************************.*************** PP TIGR00653 438 ielkrkEveelrlkvhpvElekyl 461 +e+k+ E++++r++vhp+E e+yl NCBI__GCF_000224785.1:WP_029329000.1 419 VEAKQIEWDMFRTAVHPWEREQYL 442 ***********************7 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (462 nodes) Target sequences: 1 (445 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 16.01 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.
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:
Otherwise, a candidate is "medium confidence" if either:
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:
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:
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