Alignments for a candidate for speB in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for speB in Klebsiella michiganensis M5al

Align agmatinase (EC 3.5.3.11) (characterized)
to candidate BWI76_RS21880 BWI76_RS21880 agmatinase

Query= BRENDA::Q9BSE5
         (352 letters)



>FitnessBrowser__Koxy:BWI76_RS21880
          Length = 316

 Score =  390 bits (1001), Expect = e-113
 Identities = 191/308 (62%), Positives = 232/308 (75%)

Query: 42  NQPPSPEFVARPVGVCSMMRLPVQTSPEGLDAAFIGVPLDTGTSNRPGARFGPRRIREES 101
           +QP     + R  G  +MMRLP   + +GLDAAF+G+PLD GTS R G R+GPR IR ES
Sbjct: 6   HQPQGGNEMPRFGGRATMMRLPFIDNLQGLDAAFVGIPLDIGTSQRSGTRYGPRYIRTES 65

Query: 102 VMLGTVNPSTGALPFQSLMVADLGDVNVNLYNLQDSCRRIQEAYEKIVAAGCIPLTLGGD 161
           VM+   N +TGA PF SL VAD+GDV +N YNL  S + I++ Y  + +   IPLTLGGD
Sbjct: 66  VMIRPYNMATGAAPFDSLSVADIGDVPINTYNLLKSVQIIEDYYTGLNSFPLIPLTLGGD 125

Query: 162 HTITYPILQAMAKKHGPVGLLHVDAHTDTTDKALGEKLYHGAPFRRCVDEGLLDCKRVVQ 221
           HTIT PIL+A+ KKHGPVGL+H+DAHTDT D+  GEK+ HG  FRR V+EGLLD KRVVQ
Sbjct: 126 HTITLPILRALTKKHGPVGLIHIDAHTDTNDEMFGEKIAHGTTFRRAVEEGLLDLKRVVQ 185

Query: 222 IGIRGSSTTLDPYRYNRSQGFRVVLAEDCWMKSLVPLMGEVRQQMGGKPIYISFDIDALD 281
           IG R        +++   +GFR+V AE CW KSL PLM EVRQQMG  P+Y+SFDID+LD
Sbjct: 186 IGQRAQGYAAGDFQWGVDRGFRLVQAEQCWHKSLAPLMAEVRQQMGDGPVYLSFDIDSLD 245

Query: 282 PAYAPGTGTPEIAGLTPSQALEIIRGCQGLNVMGCDLVEVSPPYDLSGNTALLAANLLFE 341
           P +APGTGTPE+ GLT  QALEI+RGC+GLN++GCDLVEVSPPYD+SGNT+ LAANLL+E
Sbjct: 246 PIWAPGTGTPEVGGLTSIQALEIVRGCRGLNLIGCDLVEVSPPYDVSGNTSQLAANLLYE 305

Query: 342 MLCALPKV 349
           MLC LP V
Sbjct: 306 MLCVLPGV 313


Lambda     K      H
   0.320    0.139    0.424 

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: 406
Number of extensions: 8
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: 352
Length of database: 316
Length adjustment: 28
Effective length of query: 324
Effective length of database: 288
Effective search space:    93312
Effective search space used:    93312
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 BWI76_RS21880 BWI76_RS21880 (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.22296.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
    1.1e-62  198.1   0.0    1.4e-62  197.8   0.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS21880  BWI76_RS21880 agmatinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS21880  BWI76_RS21880 agmatinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.8   0.0   1.4e-62   1.4e-62      14     274 ..      36     308 ..      28     309 .. 0.92

  Alignments for each domain:
  == domain 1  score: 197.8 bits;  conditional E-value: 1.4e-62
                               TIGR01230  14 evvivgiPydattsyrpGsrhgpeaireastnLeayseeld.rdlallkvvDagdlplaaGdaremvekie 83 
                                             ++  vgiP+d  ts r G+r+gp  ir+ s+ +  y+   +   ++ l v+D gd+p+ + +  ++v+ ie
  lcl|FitnessBrowser__Koxy:BWI76_RS21880  36 DAAFVGIPLDIGTSQRSGTRYGPRYIRTESVMIRPYNMATGaAPFDSLSVADIGDVPINTYNLLKSVQIIE 106
                                             55678********************************9998678******************99******* PP

                               TIGR01230  84 evveelleegkfvvaiGGeHsitlpvirAvkkkfeklavvqfDAHtDlrdefegeklshacvmrrvlelg. 153
                                             ++ + l      ++++GG+H+itlp++rA +kk++++ ++++DAHtD+ de  gek+ h ++ rr++e g 
  lcl|FitnessBrowser__Koxy:BWI76_RS21880 107 DYYTGLNSFPLIPLTLGGDHTITLPILRALTKKHGPVGLIHIDAHTDTNDEMFGEKIAHGTTFRRAVEEGl 177
                                             **999999999*********************************************************998 PP

                               TIGR01230 154 ...lnvlqigiRsg..ikeeadlarennikvlk.relede.....iaevlakvldkpvyvtiDiDvlDPaf 213
                                                ++v+qig R++     ++++ ++ + ++++  +  ++     +aev +++ d pvy+++DiD lDP +
  lcl|FitnessBrowser__Koxy:BWI76_RS21880 178 ldlKRVVQIGQRAQgyAAGDFQWGVDRGFRLVQaEQCWHKslaplMAEVRQQMGDGPVYLSFDIDSLDPIW 248
                                             8889********97335678888888888776632222224455599************************ PP

                               TIGR01230 214 aPGvgtpepgGltskellklfvlaekekkvvGlDvvEvaPvydssevtaltaaklalelll 274
                                             aPG+gtpe+gGlts ++l+  v++    +++G+D+vEv+P yd s  t  +aa+l +e+l 
  lcl|FitnessBrowser__Koxy:BWI76_RS21880 249 APGTGTPEVGGLTSIQALE-IVRGCRGLNLIGCDLVEVSPPYDVSGNTSQLAANLLYEMLC 308
                                             *******************.999************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (275 nodes)
Target sequences:                          1  (316 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: 8.82
//
[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