Alignments for a candidate for speB in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for speB in Herbaspirillum seropedicae SmR1

Align agmatinase (EC 3.5.3.11) (characterized)
to candidate HSERO_RS08555 HSERO_RS08555 agmatinase

Query= BRENDA::W5PHZ9
         (361 letters)



>FitnessBrowser__HerbieS:HSERO_RS08555
          Length = 317

 Score =  394 bits (1012), Expect = e-114
 Identities = 195/308 (63%), Positives = 231/308 (75%)

Query: 52  QPPSSEFVARSVGICSMMRLPMQATPEGLDAALVGVPLDIGTSNRPGARFGPRRIREESV 111
           QP     + R  GI +MMRLP    P GLD   VGVPLDIGTSNR G RFGPR+IR ESV
Sbjct: 7   QPLGGNVMPRFGGIATMMRLPHVEDPAGLDVGFVGVPLDIGTSNRSGTRFGPRQIRTESV 66

Query: 112 MLRTANPSTGAVPFQFLKVADLGDVNVNLYNLQDSCRLIRADYQKIVAAGCVPLTLGGDH 171
           +LR  N +T A PF  LKVADLGDV +N Y+L DS R+I   Y +I A GC  ++LGGDH
Sbjct: 67  LLRPYNMATRAAPFDSLKVADLGDVALNPYSLLDSVRMIEEAYDRIYATGCKTISLGGDH 126

Query: 172 TITYPILQAIAEKHGPVGLVHVDAHMDTADKALGEKLYHGTPFRRCVDEGLLDCKRVVQI 231
           T+T PIL+A+A   GPVGL+HVDAH D  D   GEK+ HGTPFRR  +EGLLD +RVVQI
Sbjct: 127 TLTLPILRALARYRGPVGLIHVDAHADVNDTMNGEKIAHGTPFRRAFEEGLLDPQRVVQI 186

Query: 232 GIRGSSTTLDTYRYSRSQGFRVVLAEDCWLKSLVPLMGEVRQQMGGRPIYISFDIDGLDP 291
           G+RG+    D + + R+QGFRVV AE+CW +SL PLM EVR QMG  P+Y++FDIDGLDP
Sbjct: 187 GLRGTGYHADDFDWCRAQGFRVVQAEECWHRSLAPLMEEVRAQMGDGPVYLTFDIDGLDP 246

Query: 292 AYAPGTGTPEIAGLTPSQALEIIRGCQGLNVVGCDLVEVSPPYDPSGNTALVAANLLFEM 351
           A+APGTGTPEI GLT  Q LEIIRGC+GL++V  D+VEVSPPYD +G TALVAANL +EM
Sbjct: 247 AFAPGTGTPEIGGLTVQQGLEIIRGCKGLDIVSADVVEVSPPYDQAGTTALVAANLAYEM 306

Query: 352 LCVLPKVT 359
           LC+LP VT
Sbjct: 307 LCILPGVT 314


Lambda     K      H
   0.321    0.139    0.426 

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: 430
Number of extensions: 16
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: 361
Length of database: 317
Length adjustment: 28
Effective length of query: 333
Effective length of database: 289
Effective search space:    96237
Effective search space used:    96237
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: 49 (23.5 bits)

Align candidate HSERO_RS08555 HSERO_RS08555 (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.21225.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
    8.8e-68  214.9   0.0    1.1e-67  214.6   0.0    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS08555  HSERO_RS08555 agmatinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS08555  HSERO_RS08555 agmatinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  214.6   0.0   1.1e-67   1.1e-67      17     274 ..      39     308 ..      23     309 .. 0.92

  Alignments for each domain:
  == domain 1  score: 214.6 bits;  conditional E-value: 1.1e-67
                                  TIGR01230  17 ivgiPydattsyrpGsrhgpeaireastnLeayseeld.rdlallkvvDagdlplaaGdaremvekie 83 
                                                 vg+P+d  ts r G+r+gp +ir+ s+ L  y+       ++ lkv+D+gd+ l   +  ++v +ie
  lcl|FitnessBrowser__HerbieS:HSERO_RS08555  39 FVGVPLDIGTSNRSGTRFGPRQIRTESVLLRPYNMATRaAPFDSLKVADLGDVALNPYSLLDSVRMIE 106
                                                689******************************98877588**************9999999****** PP

                                  TIGR01230  84 evveelleegkfvvaiGGeHsitlpvirAvkkkfeklavvqfDAHtDlrdefegeklshacvmrrvle 151
                                                e  +++ + g + +++GG+H++tlp++rA ++  +++ ++++DAH+D+ d  +gek+ h ++ rr++e
  lcl|FitnessBrowser__HerbieS:HSERO_RS08555 107 EAYDRIYATGCKTISLGGDHTLTLPILRALARYRGPVGLIHVDAHADVNDTMNGEKIAHGTPFRRAFE 174
                                                ******************************************************************** PP

                                  TIGR01230 152 lg....lnvlqigiRsg..ikeeadlarennikvlk.relede.....iaevlakvldkpvyvtiDiD 207
                                                 g    ++v+qig+R      +++d+ r ++ +v++  e  ++     ++ev a++ d pvy+t+DiD
  lcl|FitnessBrowser__HerbieS:HSERO_RS08555 175 EGlldpQRVVQIGLRGTgyHADDFDWCRAQGFRVVQaEECWHRslaplMEEVRAQMGDGPVYLTFDID 242
                                                9988888********75235789*********9986444433344555999***************** PP

                                  TIGR01230 208 vlDPafaPGvgtpepgGltskellklfvlaekekkvvGlDvvEvaPvydssevtaltaaklalelll 274
                                                +lDPafaPG+gtpe+gGlt +++l+   ++ k   +v +DvvEv+P yd++  tal aa+la+e+l 
  lcl|FitnessBrowser__HerbieS:HSERO_RS08555 243 GLDPAFAPGTGTPEIGGLTVQQGLE-IIRGCKGLDIVSADVVEVSPPYDQAGTTALVAANLAYEMLC 308
                                                *************************.899************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (275 nodes)
Target sequences:                          1  (317 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.82
//
[ok]

This GapMind analysis is from Sep 17 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