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_RS21925 BWI76_RS21925 agmatinase

Query= BRENDA::W5PHZ9
         (361 letters)



>FitnessBrowser__Koxy:BWI76_RS21925
          Length = 323

 Score =  262 bits (670), Expect = 8e-75
 Identities = 137/305 (44%), Positives = 187/305 (61%), Gaps = 3/305 (0%)

Query: 52  QPPSSEFVARSVGICSMMRLPMQATPEGLDAALVGVPLDIGTSNRPGARFGPRRIREESV 111
           QP   E + R  G+ +  RLP       LD  +VGVP D GT+NR G R GPR +R  S 
Sbjct: 11  QPQDGE-IPRFSGLPTFFRLPFAPQAAELDIGIVGVPWDGGTTNRAGTRHGPRELRNASS 69

Query: 112 MLRTANPSTGAVPFQFLKVADLGDVNVNLYNLQDSCRLIRADYQKIVAAGCVPLTLGGDH 171
           ++R  + +T   P+ + +V DLGDV +N  ++QDS   I A Y+ +     +PLT GGDH
Sbjct: 70  LVRRIHQTTRRSPYDYARVGDLGDVRINPVDMQDSLARIEAWYRALAEQQVMPLTAGGDH 129

Query: 172 TITYPILQAIAEKHGPVGLVHVDAHMDTADKALG-EKLYHGTPFRRCVDEGLLDCKRVVQ 230
             T PIL+A+  +  P+G++H DAH DT D   G E+  HGTPFRR V+EG+LD +R VQ
Sbjct: 130 LTTLPILRALG-RDKPLGMIHFDAHSDTNDSYFGGERFTHGTPFRRAVEEGVLDPRRTVQ 188

Query: 231 IGIRGSSTTLDTYRYSRSQGFRVVLAEDCWLKSLVPLMGEVRQQMGGRPIYISFDIDGLD 290
           IGIRG+  + D + ++   G  ++  E      +  +M   R  +G +P YISFDID LD
Sbjct: 189 IGIRGALFSADEHCWAEENGITIIRMEQVDELGIDKVMQRARAIVGEQPTYISFDIDVLD 248

Query: 291 PAYAPGTGTPEIAGLTPSQALEIIRGCQGLNVVGCDLVEVSPPYDPSGNTALVAANLLFE 350
           P YAPGTGTPEI G+T  QA   +R   GLN++G D+VEVSPP+D    T+L  A ++FE
Sbjct: 249 PVYAPGTGTPEIGGMTTLQAQRCVRQLAGLNLIGADVVEVSPPFDQGNLTSLTGATMMFE 308

Query: 351 MLCVL 355
           +LC L
Sbjct: 309 LLCQL 313


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: 364
Number of extensions: 14
Number of successful extensions: 3
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: 323
Length adjustment: 29
Effective length of query: 332
Effective length of database: 294
Effective search space:    97608
Effective search space used:    97608
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_RS21925 BWI76_RS21925 (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.12706.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
    6.3e-62  195.7   0.0    7.8e-62  195.4   0.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS21925  BWI76_RS21925 agmatinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS21925  BWI76_RS21925 agmatinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.4   0.0   7.8e-62   7.8e-62       6     274 ..      31     311 ..      27     312 .. 0.91

  Alignments for each domain:
  == domain 1  score: 195.4 bits;  conditional E-value: 7.8e-62
                               TIGR01230   6 seaeyeeAevvivgiPydattsyrpGsrhgpeaireastnLeayseeld.rdlallkvvDagdlplaaGda 75 
                                             + ++++e ++ ivg+P+d  t  r+G+rhgp  +r+as  +   +++     ++ ++v D+gd+ +   d 
  lcl|FitnessBrowser__Koxy:BWI76_RS21925  31 FAPQAAELDIGIVGVPWDGGTTNRAGTRHGPRELRNASSLVRRIHQTTRrSPYDYARVGDLGDVRINPVDM 101
                                             56889999**********************************9999998345788**************** PP

                               TIGR01230  76 remvekieevveelleegkfvvaiGGeHsitlpvirAvkkkfeklavvqfDAHtDlrdef.egeklshacv 145
                                             ++++ +ie+  + l e+  ++++ GG+H+ tlp++rA  +  ++l +++fDAH D+ d +  ge+++h ++
  lcl|FitnessBrowser__Koxy:BWI76_RS21925 102 QDSLARIEAWYRALAEQQVMPLTAGGDHLTTLPILRALGRD-KPLGMIHFDAHSDTNDSYfGGERFTHGTP 171
                                             *************************************9886.79*************87527899****** PP

                               TIGR01230 146 mrrvlelg....lnvlqigiRsgi..keeadlarennikvlkrelede......iaevlakvldkpvyvti 204
                                              rr++e g    ++++qigiR  +   +e+ +a+en+i ++++e  de      ++++ a+v ++p y+++
  lcl|FitnessBrowser__Koxy:BWI76_RS21925 172 FRRAVEEGvldpRRTVQIGIRGALfsADEHCWAEENGITIIRMEQVDElgidkvMQRARAIVGEQPTYISF 242
                                             ******99888889*******8753368999***********988887785444555667899******** PP

                               TIGR01230 205 DiDvlDPafaPGvgtpepgGltskellklfvlaekekkvvGlDvvEvaPvydssevtaltaaklalelll 274
                                             DiDvlDP +aPG+gtpe+gG+t+ ++ +  v++    +++G+DvvEv+P +d+ ++t lt a+++ ell 
  lcl|FitnessBrowser__Koxy:BWI76_RS21925 243 DIDVLDPVYAPGTGTPEIGGMTTLQAQR-CVRQLAGLNLIGADVVEVSPPFDQGNLTSLTGATMMFELLC 311
                                             ****************************.999***********************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (275 nodes)
Target sequences:                          1  (323 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: 00:00:00.00
# Mc/sec: 8.96
//
[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