GapMind for catabolism of small carbon sources

 

Alignments for a candidate for arcC in Amantichitinum ursilacus IGB-41

Align carbamate kinase (EC 2.7.2.2) (characterized)
to candidate WP_053939150.1 WG78_RS17575 carbamate kinase

Query= BRENDA::A0A0H3BY05
         (316 letters)



>NCBI__GCF_001294205.1:WP_053939150.1
          Length = 319

 Score =  261 bits (667), Expect = 2e-74
 Identities = 151/321 (47%), Positives = 197/321 (61%), Gaps = 8/321 (2%)

Query: 1   MTKQKIVVALGGNAILSTD--ASAKAQQEALISTSKSLVKLIKEGHEVIVTHGNGPQVGN 58
           M  +  VVA+GGNA++  D   S   Q EA+I +   +V LI+ G  V++THGNGPQVG 
Sbjct: 1   MKPRLAVVAVGGNALIRDDQHTSIPDQYEAVIESVSHIVPLIEAGWNVVLTHGNGPQVGF 60

Query: 59  LLLQQAAADSEKNPAMPLDTCVAMTEGSIGFWLVNALDNELQAQGIQKEVAAVVTQVIVD 118
           +L +   A  E  P +PLD  V  T+G+IG+    AL NELQ +G+ K V  +VTQ  V 
Sbjct: 61  ILRRSELAALEVAP-VPLDYAVGDTQGAIGYMFQKALTNELQRRGLIKPVITLVTQTRVS 119

Query: 119 AKDPAFENPTKPIGPFLTEEDAKKQMAESGASFKEDAGRGWRKVVPSPKPVGIKEANVIR 178
             DPAF NP KP+G FL E+ A+ +  E G +  EDAGRGWR+ V SP+P  I E+ +I 
Sbjct: 120 LSDPAFRNPAKPVGAFLDEDTARIRQRELGWTVMEDAGRGWRRTVASPQPQEILESGLIG 179

Query: 179 SLVDSGVVVVSAGGGGVPVVEDATSKSLTGVEAVIDKDFASQTLSELVDADLFIVLTGVD 238
            LV+ G VV++ GGGG+PVV D   + L GVEAVIDKD AS  L+  + ADL ++ TGV+
Sbjct: 180 QLVEQGCVVIACGGGGIPVVRD-EHQQLQGVEAVIDKDLASALLATQLGADLLLIPTGVE 238

Query: 239 NVYINFNKPDQAKLEEVTVSQMKEYITQDQFAPGSMLPKVEAAIAFVENKPN----AKAI 294
            V INF KPDQ  L ++++ + +  I Q QF  GSMLPKVEA + FVE        A  +
Sbjct: 239 QVAINFGKPDQQWLNQLSLEEAQALIEQGQFGAGSMLPKVEAILGFVEQSRQQGKAASGL 298

Query: 295 ITSLENIDNVLSANAGTQIIA 315
           ITS   I   LS   GT I A
Sbjct: 299 ITSPAAIGRALSRETGTWINA 319


Lambda     K      H
   0.311    0.129    0.349 

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: 238
Number of extensions: 11
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: 316
Length of database: 319
Length adjustment: 27
Effective length of query: 289
Effective length of database: 292
Effective search space:    84388
Effective search space used:    84388
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 48 (23.1 bits)

Align candidate WP_053939150.1 WG78_RS17575 (carbamate kinase)
to HMM TIGR00746 (arcC: carbamate kinase (EC 2.7.2.2))

# 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.carbon/TIGR00746.hmm
# target sequence database:        /tmp/gapView.4045820.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00746  [M=309]
Accession:   TIGR00746
Description: arcC: carbamate kinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.9e-112  360.2   0.1   4.4e-112  360.1   0.1    1.0  1  NCBI__GCF_001294205.1:WP_053939150.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001294205.1:WP_053939150.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  360.1   0.1  4.4e-112  4.4e-112       3     307 ..       6     317 ..       4     319 .] 0.95

  Alignments for each domain:
  == domain 1  score: 360.1 bits;  conditional E-value: 4.4e-112
                             TIGR00746   3 vvvaLGGnallqrgekasaeeqrknvekaakqlvklakrgyelvithGngPqvGalllqne.aadsvpakPld 74 
                                            vva+GGnal++ ++++s+ +q+++v ++++++v l+++g ++v+thGngPqvG +l ++e aa +v++ Pld
  NCBI__GCF_001294205.1:WP_053939150.1   6 AVVAVGGNALIRDDQHTSIPDQYEAVIESVSHIVPLIEAGWNVVLTHGNGPQVGFILRRSElAALEVAPVPLD 78 
                                           69****************************************************998876625556******* PP

                             TIGR00746  75 vlgaesqgliGYllqqalkeelakeglekkvatvltqvivdekDeaFqnPtkpigpfydeeeakrlaaekgai 147
                                            ++  +qg iGY++q+al++el+++gl k+v+t++tq+ v+  D+aF+nP kp+g f+de++a+  ++e g++
  NCBI__GCF_001294205.1:WP_053939150.1  79 YAVGDTQGAIGYMFQKALTNELQRRGLIKPVITLVTQTRVSLSDPAFRNPAKPVGAFLDEDTARIRQRELGWT 151
                                           ************************************************************************* PP

                             TIGR00746 148 lkedagrgwRrvvpsPkPkeiveaeviktLvekgvivissgGGGvPvvkdgke.lkGveaviDkDlasekLae 219
                                           + edagrgwRr v+sP+P+ei+e+  i +Lve+g +vi++gGGG+Pvv+d+++ l+GveaviDkDlas++La+
  NCBI__GCF_001294205.1:WP_053939150.1 152 VMEDAGRGWRRTVASPQPQEILESGLIGQLVEQGCVVIACGGGGIPVVRDEHQqLQGVEAVIDKDLASALLAT 224
                                           ************************************************988655******************* PP

                             TIGR00746 220 evnaDilviltdvdavyvnygkpdekkleevkveeleelakdgefaaGsmgPkveaaiefves...rgk..ka 287
                                           +++aD l+i t+v++v++n+gkpd+++l+++++ee+++l+++g+f+aGsm+Pkvea+  fve+   +gk  + 
  NCBI__GCF_001294205.1:WP_053939150.1 225 QLGADLLLIPTGVEQVAINFGKPDQQWLNQLSLEEAQALIEQGQFGAGSMLPKVEAILGFVEQsrqQGKaaSG 297
                                           *************************************************************752226774445 PP

                             TIGR00746 288 iitslekivealegkaGtvv 307
                                           +its++ i  al  ++Gt +
  NCBI__GCF_001294205.1:WP_053939150.1 298 LITSPAAIGRALSRETGTWI 317
                                           9*****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (309 nodes)
Target sequences:                          1  (319 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 13.98
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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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