GapMind for catabolism of small carbon sources

 

Aligments for a candidate for manA in Klebsiella michiganensis M5al

Align mannose-6-phosphate isomerase (EC 5.3.1.8) (characterized)
to candidate BWI76_RS16280 BWI76_RS16280 mannose-6-phosphate isomerase

Query= BRENDA::P25081
         (391 letters)



>FitnessBrowser__Koxy:BWI76_RS16280
          Length = 392

 Score =  645 bits (1664), Expect = 0.0
 Identities = 325/391 (83%), Positives = 350/391 (89%)

Query: 1   MQKLINSVQNYAWGSKTALTELYGIANPQQQPMAELWMGAHPKSSSRITTANGETVSLRD 60
           MQKLINSVQNYAWGS TALTELYGIANP   PMAELWMGAHPKSSS+I   +G   SLRD
Sbjct: 1   MQKLINSVQNYAWGSHTALTELYGIANPNNLPMAELWMGAHPKSSSQILDNSGTPRSLRD 60

Query: 61  AIEKNKTAMLGEAVANRFGELPFLFKVLCAAQPLSIQVHPNKRNSEIGFAKENAAGIPMD 120
           AI+ +K  +LGE VA RFGELPFLFKVLCAAQPLSIQVHPNK+ SEIGFAKENAAGIP+D
Sbjct: 61  AIDSDKATLLGEKVAGRFGELPFLFKVLCAAQPLSIQVHPNKQASEIGFAKENAAGIPLD 120

Query: 121 AAERNYKDPNHKPELVFALTPFLAMNAFREFSDIVSLLQPVAGAHSAIAHFLQVPNAERL 180
           AAERNYKDPNHKPELVFALTPFLAMNAFREFSDIV+LLQPVA AH AIA FL  PN E L
Sbjct: 121 AAERNYKDPNHKPELVFALTPFLAMNAFREFSDIVNLLQPVADAHPAIAQFLAQPNGEHL 180

Query: 181 SQLFASLLNMQGEEKSRALAVLKAALNSQQGEPWQTIRVISEYYPDDSGLFSPLLLNVVK 240
           SQLFASLLNM+GEEK+ AL VL+AAL+S+QGEPWQTIR+I+E+YPDDSGLFSPLLLNVVK
Sbjct: 181 SQLFASLLNMKGEEKAHALRVLQAALDSEQGEPWQTIRLIAEFYPDDSGLFSPLLLNVVK 240

Query: 241 LNPGEAMFLFAETPHAYLQGVALEVMANSDNVLRAGLTPKYIDIPELVANVKFEPKPAGE 300
           LNPGEAMFLFAETPHAYL+GVALEVMANSDNVLRAGLTPKYIDIPELVANVKF PKPAGE
Sbjct: 241 LNPGEAMFLFAETPHAYLRGVALEVMANSDNVLRAGLTPKYIDIPELVANVKFTPKPAGE 300

Query: 301 LLTAPVKSGAELDFPIPVDDFAFSLHDLALQETSIGQHSAAILFCVEGEAVLRKDEQRLV 360
           LLT PV  GAELDFPIPVDDFAFSLHDL+ Q ++I Q SAAILFCVEGEAV+ KD+  L 
Sbjct: 301 LLTQPVSRGAELDFPIPVDDFAFSLHDLSAQASTIAQDSAAILFCVEGEAVITKDKHSLT 360

Query: 361 LKPGESAFIGADESPVNASGTGRLARVYNKL 391
           LKPGESAFIG +ESPV  SG GR+ARV+NKL
Sbjct: 361 LKPGESAFIGCNESPVQVSGYGRVARVFNKL 391


Lambda     K      H
   0.317    0.132    0.379 

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: 604
Number of extensions: 14
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: 391
Length of database: 392
Length adjustment: 31
Effective length of query: 360
Effective length of database: 361
Effective search space:   129960
Effective search space used:   129960
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 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate BWI76_RS16280 BWI76_RS16280 (mannose-6-phosphate isomerase)
to HMM TIGR00218 (manA: mannose-6-phosphate isomerase, class I (EC 5.3.1.8))

# 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/TIGR00218.hmm
# target sequence database:        /tmp/gapView.3372.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00218  [M=359]
Accession:   TIGR00218
Description: manA: mannose-6-phosphate isomerase, class I
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   1.5e-131  424.8   0.0   1.7e-131  424.6   0.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS16280  BWI76_RS16280 mannose-6-phosphat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS16280  BWI76_RS16280 mannose-6-phosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  424.6   0.0  1.7e-131  1.7e-131       2     354 ..       3     382 ..       1     387 [. 0.97

  Alignments for each domain:
  == domain 1  score: 424.6 bits;  conditional E-value: 1.7e-131
                               TIGR00218   2 kflfrvqknlkerdWGkgtaladllgysipskq.taElWagaHkkgsSkvqng..kkvsLrdliekhksel 69 
                                             k++++v    ++++WG+ tal++l+g ++p +  +aElW+gaH+k+sS+++ +     sLrd i+++k +l
  lcl|FitnessBrowser__Koxy:BWI76_RS16280   3 KLINSV----QNYAWGSHTALTELYGIANPNNLpMAELWMGAHPKSSSQILDNsgTPRSLRDAIDSDKATL 69 
                                             345555....559*****************9877****************99656889************* PP

                               TIGR00218  70 lGkaeadrf.elPlLvkvLsaekplsiqvHPdkalakigyake..........krnYkDknhkpelvialt 129
                                             lG+++a rf elP+L+kvL+a++plsiqvHP+k+ ++ig+ake          +rnYkD+nhkpelv+alt
  lcl|FitnessBrowser__Koxy:BWI76_RS16280  70 LGEKVAGRFgELPFLFKVLCAAQPLSIQVHPNKQASEIGFAKEnaagipldaaERNYKDPNHKPELVFALT 140
                                             *********************************************************************** PP

                               TIGR00218 130 dfealkgfkp.......Lkriaelh.........eeaerlgkteawviiasdekikeaaeilkealknske 184
                                             +f+a+++f++       L+++a++h         +++e+l++ +a+++++++e++ +a ++l+ al++++ 
  lcl|FitnessBrowser__Koxy:BWI76_RS16280 141 PFLAMNAFREfsdivnlLQPVADAHpaiaqflaqPNGEHLSQLFASLLNMKGEEKAHALRVLQAALDSEQG 211
                                             **********999999999999999********************************************** PP

                               TIGR00218 185 elkekiqrl..iypedvglfkgllLnrvklkpgeaiyvrsgtvHAykggdvlEvmanSdnvvragltdkyl 253
                                             e++++i+++  +yp+d+glf++llLn+vkl+pgea++++++t+HAy++g++lEvmanSdnv+raglt+ky+
  lcl|FitnessBrowser__Koxy:BWI76_RS16280 212 EPWQTIRLIaeFYPDDSGLFSPLLLNVVKLNPGEAMFLFAETPHAYLRGVALEVMANSDNVLRAGLTPKYI 282
                                             ******999************************************************************** PP

                               TIGR00218 254 dvkklvevltveekpeeklkeqkqkegaevlflvpieefavlktdlsekaelksqdsalillvleGdglil 324
                                             d+++lv++++++ kp+ +l +q++ +gae++f++p+++fa++ +dls +a+++ qdsa+il+++eG+++i 
  lcl|FitnessBrowser__Koxy:BWI76_RS16280 283 DIPELVANVKFTPKPAGELLTQPVSRGAELDFPIPVDDFAFSLHDLSAQASTIAQDSAAILFCVEGEAVIT 353
                                             *********************************************************************** PP

                               TIGR00218 325 sgekklklkkGesfliaakleevtiegede 354
                                             +++++l lk+Ges++i+ ++++v++ g+ +
  lcl|FitnessBrowser__Koxy:BWI76_RS16280 354 KDKHSLTLKPGESAFIGCNESPVQVSGY-G 382
                                             **************************98.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (359 nodes)
Target sequences:                          1  (392 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: 10.42
//
[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:

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:

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:

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, or view the source code.

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