Alignments for a candidate for speB in Trichodesmium erythraeum IMS101

GapMind for catabolism of small carbon sources

Alignments for a candidate for speB in Trichodesmium erythraeum IMS101

Align agmatinase (EC 3.5.3.11) (characterized)
to candidate WP_011613157.1 TERY_RS18140 agmatinase

Query= BRENDA::Q57757
         (284 letters)



>NCBI__GCF_000014265.1:WP_011613157.1
          Length = 303

 Score =  149 bits (376), Expect = 7e-41
 Identities = 102/276 (36%), Positives = 153/276 (55%), Gaps = 15/276 (5%)

Query: 18  YEEAEGVIFSIPYDETTSFKPGAREGGNAIRTASWGLETYSPILDRD--LAELKYCDLKD 75
           Y  A+ VI  IPY+ TT+++ G   G   +  AS  LE Y   LDR+  L    Y     
Sbjct: 21  YTTAKVVIVPIPYEATTTYRRGCVNGPAVLLNASQQLECYDEELDRETGLEVGIYTHEPI 80

Query: 76  LDLYGSQE----EIFGTIHSVSREILKENKKIIVFGGEHSITYPIIKAVKDIYDD--FIV 129
            D    ++    ++         +++ + K +I  GGEHSIT  I+KA K +Y D  F V
Sbjct: 81  ADTRNGKKITPLDMLKVTQETVEKLVSDGKFVIAIGGEHSITNGIVKAYKKLYFDEPFTV 140

Query: 130 IQFDAHCDLRDEYLGNKLSHACVMRRVYELTKNIFQFGIRSGDKEEWDLARKNNLYL--- 186
           IQ DAH DLR EY G+  +HACVMRR++E+   + Q GIR+  KEE DL +  NL +   
Sbjct: 141 IQIDAHGDLRYEYEGSIYNHACVMRRIFEMGLPMVQIGIRAICKEEADLIKDKNLTVFKA 200

Query: 187 KMDLMNKDDLEYIKS--LDKPIYVTIDIDVLDPAYAPGTGTPEPCGFSTRELFNSLYLLE 244
           +   +  D +E + S    K +++TID+D +DP   PG GTPEP G +   L   L  + 
Sbjct: 201 REIAIQPDWMERVISSIQTKNVFLTIDLDGIDPTLIPGVGTPEPGGLNWYSLTTFLRRIF 260

Query: 245 EVKDKIIGFDIVEVSPIYDIANITAITAAKIARELM 280
           E+  +++G DI+E++PI D + ++  TAAK+  +L+
Sbjct: 261 ELY-QVLGCDIMELAPITD-SVVSEFTAAKLVYKLV 294


Lambda     K      H
   0.321    0.141    0.413 

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: 193
Number of extensions: 10
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: 284
Length of database: 303
Length adjustment: 26
Effective length of query: 258
Effective length of database: 277
Effective search space:    71466
Effective search space used:    71466
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 (21.8 bits)
S2: 48 (23.1 bits)

Align candidate WP_011613157.1 TERY_RS18140 (agmatinase)
to HMM TIGR01230 (speB: agmatinase (EC 3.5.3.11))

# 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/TIGR01230.hmm
# target sequence database:        /tmp/gapView.25268.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01230  [M=275]
Accession:   TIGR01230
Description: agmatinase: agmatinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    6.7e-91  290.7   0.0      8e-91  290.4   0.0    1.0  1  lcl|NCBI__GCF_000014265.1:WP_011613157.1  TERY_RS18140 agmatinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000014265.1:WP_011613157.1  TERY_RS18140 agmatinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  290.4   0.0     8e-91     8e-91       5     274 ..      16     295 ..      12     296 .. 0.93

  Alignments for each domain:
  == domain 1  score: 290.4 bits;  conditional E-value: 8e-91
                                 TIGR01230   5 eseaeyeeAevvivgiPydattsyrpGsrhgpeaireastnLeayseeldrdlal.......lkvvDag 66 
                                               e e++y  A+vviv+iPy+att yr+G+  gp+ +++as++Le y+eeldr+ +l        +++D+ 
  lcl|NCBI__GCF_000014265.1:WP_011613157.1  16 EIEPDYTTAKVVIVPIPYEATTTYRRGCVNGPAVLLNASQQLECYDEELDRETGLevgiythEPIADTR 84 
                                               56899*********************************************8877765666666777777 PP

                                 TIGR01230  67 dlplaaGdaremvekieevveelleegkfvvaiGGeHsitlpvirAvkkkf..eklavvqfDAHtDlrd 133
                                               + +  +  + +m++  +e+ve+l+ +gkfv+aiGGeHsit ++++A kk +  e+++v+q+DAH+Dlr 
  lcl|NCBI__GCF_000014265.1:WP_011613157.1  85 NGKKIT--PLDMLKVTQETVEKLVSDGKFVIAIGGEHSITNGIVKAYKKLYfdEPFTVIQIDAHGDLRY 151
                                               766643..45899999*********************************654568************** PP

                                 TIGR01230 134 efegeklshacvmrrvlelglnvlqigiRsgikeeadlarennikvlk.relede...iaevlakvldk 198
                                               e+eg+ ++hacvmrr++e+gl+++qigiR+++keeadl++++n+ v+k re++ +   +++v+ ++ +k
  lcl|NCBI__GCF_000014265.1:WP_011613157.1 152 EYEGSIYNHACVMRRIFEMGLPMVQIGIRAICKEEADLIKDKNLTVFKaREIAIQpdwMERVISSIQTK 220
                                               ************************************************9**9977777999******** PP

                                 TIGR01230 199 pvyvtiDiDvlDPafaPGvgtpepgGltskellklfvlaekekkvvGlDvvEvaPvydssevtaltaak 267
                                               +v++tiD+D++DP+ +PGvgtpepgGl+++ l  ++++ ++  +v G+D++E+aP +  s+v+++taak
  lcl|NCBI__GCF_000014265.1:WP_011613157.1 221 NVFLTIDLDGIDPTLIPGVGTPEPGGLNWYSLTTFLRRIFELYQVLGCDIMELAP-ITDSVVSEFTAAK 288
                                               *******************************************************.66799******** PP

                                 TIGR01230 268 lalelll 274
                                               l+++l++
  lcl|NCBI__GCF_000014265.1:WP_011613157.1 289 LVYKLVG 295
                                               ****986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (275 nodes)
Target sequences:                          1  (303 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: 00:00:00.00
# Mc/sec: 11.32
//
[ok]

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

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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

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 catabolism of small carbon sources