Alignments for a candidate for carA in Novosphingobium barchaimii LL02

GapMind for Amino acid biosynthesis

Alignments for a candidate for carA in Novosphingobium barchaimii LL02

Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate WP_059150258.1 V474_RS04270 glutamine-hydrolyzing carbamoyl-phosphate synthase small subunit

Query= SwissProt::P0A6F1
         (382 letters)



>NCBI__GCF_001046635.1:WP_059150258.1
          Length = 388

 Score =  353 bits (906), Expect = e-102
 Identities = 192/375 (51%), Positives = 241/375 (64%), Gaps = 7/375 (1%)

Query: 4   SALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHIGNV 63
           + +LVL DG    GR  G  G +VGEV FNT+MTGYQE++TDPSY+ QIVT T+PHIGNV
Sbjct: 16  TGVLVLSDGHVVWGRGFGHVGESVGEVCFNTAMTGYQEVMTDPSYAGQIVTFTFPHIGNV 75

Query: 64  GTNDADEESSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTRLLR 123
           G ND D ES    A G V+R+   ++S+FR   +   +L     V ++ +DTR LTR +R
Sbjct: 76  GVNDEDLESKVDGAVGCVVREDVTLSSSFRADAEFGPWLASKGKVGLSGVDTRALTRRIR 135

Query: 124 EKGAQNGCIIAGD---NPDAALALEKARAFPGLNGMDLAKEVTTAEAYSWTQGSWTLTGG 180
             GA N  +IA D   N D    +++A+ +PGL GMDLAK V+      W    WTL  G
Sbjct: 136 MAGAPNA-VIAHDPEGNFDIPALIKRAQEWPGLEGMDLAKIVSREIQEGWEGSIWTLGAG 194

Query: 181 LPEAKKEDELPFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDGIFLSN 240
              A + D  P HVVA DFGAK NI R LV  G R+T+VPA+T+ + +L + P G+FLSN
Sbjct: 195 YG-AGEGDARP-HVVAMDFGAKDNIFRNLVKAGARVTVVPAETTLDQILALEPAGVFLSN 252

Query: 241 GPGDPAPCD-YAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHPVKD 299
           GPGDPA    YA+  IQ  +E D+PVFGICLGHQ+L LA+GA T KM  GH G NHPVK 
Sbjct: 253 GPGDPAATGKYAVPVIQSLIERDVPVFGICLGHQMLGLAAGATTSKMHQGHRGANHPVKR 312

Query: 300 VEKNVVMITAQNHGFAVDEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHPEASPG 359
           +   VV IT+ NHGFAVD  +LP  +  TH SLFDG+  GI    K AF  Q HPEASPG
Sbjct: 313 LADGVVEITSMNHGFAVDNTSLPDGVEETHVSLFDGSNCGISIKGKRAFGVQYHPEASPG 372

Query: 360 PHDAAPLFDHFIELI 374
           P D+  LFD F+ ++
Sbjct: 373 PQDSFYLFDKFVGML 387


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: 453
Number of extensions: 22
Number of successful extensions: 4
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: 388
Length adjustment: 30
Effective length of query: 352
Effective length of database: 358
Effective search space:   126016
Effective search space used:   126016
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_059150258.1 V474_RS04270 (glutamine-hydrolyzing 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.2038976.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.3e-128  414.1   0.0   2.6e-128  413.9   0.0    1.0  1  NCBI__GCF_001046635.1:WP_059150258.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001046635.1:WP_059150258.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  413.9   0.0  2.6e-128  2.6e-128       2     358 ..      18     386 ..      17     388 .] 0.94

  Alignments for each domain:
  == domain 1  score: 413.9 bits;  conditional E-value: 2.6e-128
                             TIGR01368   2 tlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaeskkikvk 74 
                                           +lvl+dG+v+ g++fg+ +e vGev+FnT+mtGYqE++tDpsY+gqiv++t p+ign+gvn+ed esk   + 
  NCBI__GCF_001046635.1:WP_059150258.1  18 VLVLSDGHVVWGRGFGHVGESVGEVCFNTAMTGYQEVMTDPSYAGQIVTFTFPHIGNVGVNDEDLESKVDGAV 90 
                                           69*********************************************************************** PP

                             TIGR01368  75 glvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavistekse...keelvekake 144
                                           g vv+e  +  s++ra  ++  +l+++g v++ gvDTRal++++R +g+ +avi+++ +       l+++a+e
  NCBI__GCF_001046635.1:WP_059150258.1  91 GCVVREDVTLSSSFRADAEFGPWLASKGKVGLSGVDTRALTRRIRMAGAPNAVIAHDPEGnfdIPALIKRAQE 163
                                           *******************************************************998765546688999999 PP

                             TIGR01368 145 spkvkevnlvkevstkeayeleq......k...akkegkklrvvvidlGvKenilreLvkrgvevtvvpadts 208
                                            p +++++l+k vs + +  +e           a + + + +vv++d+G K ni r+Lvk g++vtvvpa+t+
  NCBI__GCF_001046635.1:WP_059150258.1 164 WPGLEGMDLAKIVSREIQEGWEGsiwtlgAgygAGEGDARPHVVAMDFGAKDNIFRNLVKAGARVTVVPAETT 236
                                           ****************99999986665551555555666689******************************* PP

                             TIGR01368 209 aeeikklnpdgillsnGPGdPaav.eeaietvkklleakiPifGIclGhqllalalgaktyklkfGhrGaNhp 280
                                           +++i +l+p g++lsnGPGdPaa  ++a+  +++l+e+++P+fGIclGhq+l+la+ga t k++ GhrGaNhp
  NCBI__GCF_001046635.1:WP_059150258.1 237 LDQILALEPAGVFLSNGPGDPAATgKYAVPVIQSLIERDVPVFGICLGHQMLGLAAGATTSKMHQGHRGANHP 309
                                           *********************8763678999****************************************** PP

                             TIGR01368 281 vkdlktgrveitsqNHgyavdeeslkeeelevthvnlnDgtveglehkelpvfsvQyHPeaspGphdteylFd 353
                                           vk l++g veits NHg+avd+ sl+ + +e thv+l+Dg++ g++ k +++f vQyHPeaspGp+d+ ylFd
  NCBI__GCF_001046635.1:WP_059150258.1 310 VKRLADGVVEITSMNHGFAVDNTSLPDG-VEETHVSLFDGSNCGISIKGKRAFGVQYHPEASPGPQDSFYLFD 381
                                           ************************8855.******************************************** PP

                             TIGR01368 354 efvel 358
                                           +fv +
  NCBI__GCF_001046635.1:WP_059150258.1 382 KFVGM 386
                                           **965 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (361 nodes)
Target sequences:                          1  (388 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: 16.80
//
[ok]

This GapMind analysis is from Jul 26 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