GapMind for Amino acid biosynthesis

 

Alignments for a candidate for carA in Magnetospirillum magneticum AMB-1

Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate WP_050750618.1 AMB_RS03600 carbamoyl-phosphate synthase small subunit

Query= SwissProt::P0A6F1
         (382 letters)



>NCBI__GCF_000009985.1:WP_050750618.1
          Length = 401

 Score =  408 bits (1048), Expect = e-118
 Identities = 208/375 (55%), Positives = 266/375 (70%), Gaps = 10/375 (2%)

Query: 7   LVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHIGNVGTN 66
           LVL DG+   G+ IGATGS VGEVVF T MTGYQE LTDPS++ Q++T T+PH+GNVGTN
Sbjct: 30  LVLADGSVLWGKGIGATGSNVGEVVFTTGMTGYQETLTDPSFAGQVITFTFPHVGNVGTN 89

Query: 67  DADEESSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTRLLREKG 126
             D E++   A+GL++R      +N+R+ + L S+LK +NIV +  +DTR LTR +R KG
Sbjct: 90  VEDLETTTPAARGLILRADITDPANWRSAKHLDSWLKANNIVGLCGVDTRALTRRIRAKG 149

Query: 127 AQNGCIIAGDNPDAALALE----KARAFPGLNGMDLAKEVTTAEAYSWTQGSWTLTGGLP 182
           A NG I+  + PD A  L     KA  +PGL GMDLA++VT A+ YSW +  W+L GG  
Sbjct: 150 APNGVIV--NAPDGAFDLPALWGKAAGWPGLEGMDLARDVTCAQTYSWDETEWSLRGGYG 207

Query: 183 EAKKEDELPFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDGIFLSNGP 242
              K     FHVVA DFGAKRNILR L + GC++T++PA+ +AE VL + PDG+FLSNGP
Sbjct: 208 RQAKPR---FHVVAVDFGAKRNILRCLAETGCKVTVLPAEATAEQVLALEPDGVFLSNGP 264

Query: 243 GDPAPCD-YAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHPVKDVE 301
           GDPA    YA+  IQ  +++  P+FGICLGHQ+L LA GAKT KM  GH G NHPVKD+E
Sbjct: 265 GDPAATGTYAVPMIQGVIKSGKPLFGICLGHQMLGLALGAKTFKMDTGHRGANHPVKDLE 324

Query: 302 KNVVMITAQNHGFAVDEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHPEASPGPH 361
              V IT+QNHGF VDE +LPA ++VTH+SLFDG+++GI    KP FS Q HPEASPGP 
Sbjct: 325 TGKVEITSQNHGFVVDEKSLPAGVKVTHRSLFDGSVEGIAVDGKPVFSVQYHPEASPGPQ 384

Query: 362 DAAPLFDHFIELIEQ 376
           DA  LF+ F+ L+E+
Sbjct: 385 DAHYLFERFVGLMEK 399


Lambda     K      H
   0.318    0.135    0.400 

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: 505
Number of extensions: 20
Number of successful extensions: 5
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: 382
Length of database: 401
Length adjustment: 31
Effective length of query: 351
Effective length of database: 370
Effective search space:   129870
Effective search space used:   129870
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate WP_050750618.1 AMB_RS03600 (carbamoyl-phosphate synthase small subunit)
to HMM TIGR01368 (carA: carbamoyl-phosphate synthase, small subunit (EC 6.3.5.5))

# 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/TIGR01368.hmm
# target sequence database:        /tmp/gapView.3928894.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01368  [M=361]
Accession:   TIGR01368
Description: CPSaseIIsmall: carbamoyl-phosphate synthase, small subunit
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.7e-139  450.7   0.0     2e-139  450.5   0.0    1.0  1  lcl|NCBI__GCF_000009985.1:WP_050750618.1  AMB_RS03600 carbamoyl-phosphate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_050750618.1  AMB_RS03600 carbamoyl-phosphate synthase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  450.5   0.0    2e-139    2e-139       2     360 ..      29     398 ..      28     399 .. 0.94

  Alignments for each domain:
  == domain 1  score: 450.5 bits;  conditional E-value: 2e-139
                                 TIGR01368   2 tlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaeskk 70 
                                                lvl+dG+v+ gk++ga+++ vGevvF+T+mtGYqE+ltDps++gq++++t p++gn+g+n ed e ++
  lcl|NCBI__GCF_000009985.1:WP_050750618.1  29 ALVLADGSVLWGKGIGATGSNVGEVVFTTGMTGYQETLTDPSFAGQVITFTFPHVGNVGTNVEDLETTT 97 
                                               69******************************************************************* PP

                                 TIGR01368  71 ikvkglvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavistekse...ke 136
                                               + ++gl+++   +++ n+r+ + L+++lk ++iv++ gvDTRal++++R kg+ ++vi+++        
  lcl|NCBI__GCF_000009985.1:WP_050750618.1  98 PAARGLILRADITDPANWRSAKHLDSWLKANNIVGLCGVDTRALTRRIRAKGAPNGVIVNAPDGafdLP 166
                                               ***********************************************************9987644345 PP

                                 TIGR01368 137 elvekakespkvkevnlvkevstkeayeleq...k.....akkegkklrvvvidlGvKenilreLvkrg 197
                                                l  ka+  p +++++l+++v+++++y++ +   +      ++ + + +vv++d+G K+nilr+L+++g
  lcl|NCBI__GCF_000009985.1:WP_050750618.1 167 ALWGKAAGWPGLEGMDLARDVTCAQTYSWDEtewSlrggyGRQAKPRFHVVAVDFGAKRNILRCLAETG 235
                                               5667788899********************965515566445555569********************* PP

                                 TIGR01368 198 vevtvvpadtsaeeikklnpdgillsnGPGdPaav.eeaietvkklleakiPifGIclGhqllalalga 265
                                               ++vtv+pa+++ae++ +l+pdg++lsnGPGdPaa  ++a+ +++ ++++ +P+fGIclGhq+l+lalga
  lcl|NCBI__GCF_000009985.1:WP_050750618.1 236 CKVTVLPAEATAEQVLALEPDGVFLSNGPGDPAATgTYAVPMIQGVIKSGKPLFGICLGHQMLGLALGA 304
                                               ********************************876367899**************************** PP

                                 TIGR01368 266 ktyklkfGhrGaNhpvkdlktgrveitsqNHgyavdeeslkeeelevthvnlnDgtveglehkelpvfs 334
                                               kt+k+  GhrGaNhpvkdl+tg+veitsqNHg++vde+sl+++ ++vth++l+Dg+veg++   +pvfs
  lcl|NCBI__GCF_000009985.1:WP_050750618.1 305 KTFKMDTGHRGANHPVKDLETGKVEITSQNHGFVVDEKSLPAG-VKVTHRSLFDGSVEGIAVDGKPVFS 372
                                               ***************************************9977.************************* PP

                                 TIGR01368 335 vQyHPeaspGphdteylFdefvelik 360
                                               vQyHPeaspGp+d++ylF++fv l++
  lcl|NCBI__GCF_000009985.1:WP_050750618.1 373 VQYHPEASPGPQDAHYLFERFVGLME 398
                                               **********************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (361 nodes)
Target sequences:                          1  (401 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 23.46
//
[ok]

This GapMind analysis is from Apr 09 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:

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:

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