Alignments for a candidate for galU in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for galU in Klebsiella michiganensis M5al

Align UTP--glucose-1-phosphate uridylyltransferase; EC 2.7.7.9 (characterized)
to candidate BWI76_RS17270 BWI76_RS17270 UTP--glucose-1-phosphate uridylyltransferase

Query= CharProtDB::CH_021667
         (302 letters)



>FitnessBrowser__Koxy:BWI76_RS17270
          Length = 300

 Score =  562 bits (1448), Expect = e-165
 Identities = 279/296 (94%), Positives = 290/296 (97%)

Query: 1   MAAINTKVKKAVIPVAGLGTRMLPATKAIPKEMLPLVDKPLIQYVVNECIAAGITEIVLV 60
           MAA+N+KV+KAVIPVAGLGTRMLPATKAIPKEMLPLVDKPLIQYVVNECIAAGITEIVLV
Sbjct: 1   MAALNSKVRKAVIPVAGLGTRMLPATKAIPKEMLPLVDKPLIQYVVNECIAAGITEIVLV 60

Query: 61  THSSKNSIENHFDTSFELEAMLEKRVKRQLLDEVQSICPPHVTIMQVRQGLAKGLGHAVL 120
           THSSKNSIENHFDTSFELEAMLEKRVKRQLL+EVQSICPPHVTIMQVRQGLAKGLGHAVL
Sbjct: 61  THSSKNSIENHFDTSFELEAMLEKRVKRQLLEEVQSICPPHVTIMQVRQGLAKGLGHAVL 120

Query: 121 CAHPVVGDEPVAVILPDVILDEYESDLSQDNLAEMIRRFDETGHSQIMVEPVADVTAYGV 180
           CAHPVVGDEPVAVILPDVILDEYESDLS+DNLAEM+ RFDETG SQIMVEPVADVTAYGV
Sbjct: 121 CAHPVVGDEPVAVILPDVILDEYESDLSRDNLAEMMARFDETGASQIMVEPVADVTAYGV 180

Query: 181 VDCKGVELAPGESVPMVGVVEKPKADVAPSNLAIVGRYVLSADIWPLLAKTPPGAGDEIQ 240
           VDCKG+ L PGESVPMVGVVEKPKADVAPSNLA+VGRYVLSADIWPLLAKTPPGAGDEIQ
Sbjct: 181 VDCKGLALQPGESVPMVGVVEKPKADVAPSNLAVVGRYVLSADIWPLLAKTPPGAGDEIQ 240

Query: 241 LTDAIDMLIEKETVEAYHMKGKSHDCGNKLGYMQAFVEYGIRHNTLGTEFKAWLEE 296
           LTDAIDMLIEKETVEAYHMKGKSHDCGNKLGYMQAFVEYG+RH +LG EFKAWLE+
Sbjct: 241 LTDAIDMLIEKETVEAYHMKGKSHDCGNKLGYMQAFVEYGVRHKSLGEEFKAWLEK 296


Lambda     K      H
   0.317    0.135    0.391 

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: 463
Number of extensions: 17
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: 302
Length of database: 300
Length adjustment: 27
Effective length of query: 275
Effective length of database: 273
Effective search space:    75075
Effective search space used:    75075
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)

Align candidate BWI76_RS17270 BWI76_RS17270 (UTP--glucose-1-phosphate uridylyltransferase)
to HMM TIGR01099 (galU: UTP--glucose-1-phosphate uridylyltransferase (EC 2.7.7.9))

# 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/TIGR01099.hmm
# target sequence database:        /tmp/gapView.1801.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01099  [M=261]
Accession:   TIGR01099
Description: galU: UTP--glucose-1-phosphate uridylyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   2.7e-119  383.5   0.1   3.1e-119  383.3   0.1    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS17270  BWI76_RS17270 UTP--glucose-1-pho


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS17270  BWI76_RS17270 UTP--glucose-1-phosphate uridylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  383.3   0.1  3.1e-119  3.1e-119       1     261 []       8     275 ..       8     275 .. 0.98

  Alignments for each domain:
  == domain 1  score: 383.3 bits;  conditional E-value: 3.1e-119
                               TIGR01099   1 irkaviPaaGlGtrlLPatkaiPkemlpivdkPliqyvveeaveaGieeivlvtgrskraiedhfDtsyel 71 
                                             +rkaviP+aGlGtr+LPatkaiPkemlp+vdkPliqyvv+e+++aGi+eivlvt++sk++ie+hfDts+el
  lcl|FitnessBrowser__Koxy:BWI76_RS17270   8 VRKAVIPVAGLGTRMLPATKAIPKEMLPLVDKPLIQYVVNECIAAGITEIVLVTHSSKNSIENHFDTSFEL 78 
                                             79********************************************************************* PP

                               TIGR01099  72 eaklekknkeellkevrkiael.atilyvrqkeakGLGhavllaeelvgdepfavllgDdlvseeee.... 137
                                             ea+lek+ k++ll+ev++i++  +ti++vrq  akGLGhavl+a+++vgdep+av+l+D++++e e+    
  lcl|FitnessBrowser__Koxy:BWI76_RS17270  79 EAMLEKRVKRQLLEEVQSICPPhVTIMQVRQGLAKGLGHAVLCAHPVVGDEPVAVILPDVILDEYESdlsr 149
                                             ********************988*****************************************9998999 PP

                               TIGR01099 138 .alkqlielyektgasiiaveevpkeevskYGvidgeeveeelye...vkdlvekPkpeeapsnlaivGrY 204
                                              +l+++++++++tgas+i+ve v+  +v++YGv+d++++  +  e   +  +vekPk++ apsnla+vGrY
  lcl|FitnessBrowser__Koxy:BWI76_RS17270 150 dNLAEMMARFDETGASQIMVEPVA--DVTAYGVVDCKGLALQPGEsvpMVGVVEKPKADVAPSNLAVVGRY 218
                                             99*********************9..9***********887776666699********************* PP

                               TIGR01099 205 vltpeifelleetkaGkggeiqltDalrlllekeevlavklkgkryDvGdklgylka 261
                                             vl+++i+ ll++t++G+g+eiqltDa+++l+eke+v+a+++kgk++D+G+klgy++a
  lcl|FitnessBrowser__Koxy:BWI76_RS17270 219 VLSADIWPLLAKTPPGAGDEIQLTDAIDMLIEKETVEAYHMKGKSHDCGNKLGYMQA 275
                                             *******************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (261 nodes)
Target sequences:                          1  (300 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: 10.30
//
[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