Alignments for a candidate for manA in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for manA in Escherichia coli BW25113

Align mannose-6-phosphate isomerase (EC 5.3.1.8) (characterized)
to candidate 15734 b1613 mannose-6-phosphate isomerase (VIMSS)

Query= ecocyc::MANNPISOM-MONOMER
         (391 letters)



>FitnessBrowser__Keio:15734
          Length = 391

 Score =  772 bits (1994), Expect = 0.0
 Identities = 391/391 (100%), Positives = 391/391 (100%)

Query: 1   MQKLINSVQNYAWGSKTALTELYGMENPSSQPMAELWMGAHPKSSSRVQNAAGDIVSLRD 60
           MQKLINSVQNYAWGSKTALTELYGMENPSSQPMAELWMGAHPKSSSRVQNAAGDIVSLRD
Sbjct: 1   MQKLINSVQNYAWGSKTALTELYGMENPSSQPMAELWMGAHPKSSSRVQNAAGDIVSLRD 60

Query: 61  VIESDKSTLLGEAVAKRFGELPFLFKVLCAAQPLSIQVHPNKHNSEIGFAKENAAGIPMD 120
           VIESDKSTLLGEAVAKRFGELPFLFKVLCAAQPLSIQVHPNKHNSEIGFAKENAAGIPMD
Sbjct: 61  VIESDKSTLLGEAVAKRFGELPFLFKVLCAAQPLSIQVHPNKHNSEIGFAKENAAGIPMD 120

Query: 121 AAERNYKDPNHKPELVFALTPFLAMNAFREFSEIVSLLQPVAGAHPAIAHFLQQPDAERL 180
           AAERNYKDPNHKPELVFALTPFLAMNAFREFSEIVSLLQPVAGAHPAIAHFLQQPDAERL
Sbjct: 121 AAERNYKDPNHKPELVFALTPFLAMNAFREFSEIVSLLQPVAGAHPAIAHFLQQPDAERL 180

Query: 181 SELFASLLNMQGEEKSRALAILKSALDSQQGEPWQTIRLISEFYPEDSGLFSPLLLNVVK 240
           SELFASLLNMQGEEKSRALAILKSALDSQQGEPWQTIRLISEFYPEDSGLFSPLLLNVVK
Sbjct: 181 SELFASLLNMQGEEKSRALAILKSALDSQQGEPWQTIRLISEFYPEDSGLFSPLLLNVVK 240

Query: 241 LNPGEAMFLFAETPHAYLQGVALEVMANSDNVLRAGLTPKYIDIPELVANVKFEAKPANQ 300
           LNPGEAMFLFAETPHAYLQGVALEVMANSDNVLRAGLTPKYIDIPELVANVKFEAKPANQ
Sbjct: 241 LNPGEAMFLFAETPHAYLQGVALEVMANSDNVLRAGLTPKYIDIPELVANVKFEAKPANQ 300

Query: 301 LLTQPVKQGAELDFPIPVDDFAFSLHDLSDKETTISQQSAAILFCVEGDATLWKGSQQLQ 360
           LLTQPVKQGAELDFPIPVDDFAFSLHDLSDKETTISQQSAAILFCVEGDATLWKGSQQLQ
Sbjct: 301 LLTQPVKQGAELDFPIPVDDFAFSLHDLSDKETTISQQSAAILFCVEGDATLWKGSQQLQ 360

Query: 361 LKPGESAFIAANESPVTVKGHGRLARVYNKL 391
           LKPGESAFIAANESPVTVKGHGRLARVYNKL
Sbjct: 361 LKPGESAFIAANESPVTVKGHGRLARVYNKL 391


Lambda     K      H
   0.316    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: 685
Number of extensions: 13
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: 391
Length adjustment: 31
Effective length of query: 360
Effective length of database: 360
Effective search space:   129600
Effective search space used:   129600
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 15734 b1613 (mannose-6-phosphate isomerase (VIMSS))
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.23523.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   1.4e-150  487.4   0.0   1.6e-150  487.2   0.0    1.0  1  lcl|FitnessBrowser__Keio:15734  b1613 mannose-6-phosphate isomer


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:15734  b1613 mannose-6-phosphate isomerase (VIMSS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  487.2   0.0  1.6e-150  1.6e-150       2     356 ..       3     384 ..       1     387 [. 0.97

  Alignments for each domain:
  == domain 1  score: 487.2 bits;  conditional E-value: 1.6e-150
                       TIGR00218   2 kflfrvqknlkerdWGkgtaladllgysipskq.taElWagaHkkgsSkvqng..kkvsLrdliekhksellGkaeadr 77 
                                     k++++v    ++++WG++tal++l+g+++ps+q +aElW+gaH+k+sS+vqn+  ++vsLrd+ie++ks+llG+a+a+r
  lcl|FitnessBrowser__Keio:15734   3 KLINSV----QNYAWGSKTALTELYGMENPSSQpMAELWMGAHPKSSSRVQNAagDIVSLRDVIESDKSTLLGEAVAKR 77 
                                     345555....559******************999******************547************************ PP

                       TIGR00218  78 f.elPlLvkvLsaekplsiqvHPdkalakigyake..........krnYkDknhkpelvialtdfealkgfkp...... 139
                                     f elP+L+kvL+a++plsiqvHP+k++++ig+ake          +rnYkD+nhkpelv+alt+f+a+++f++      
  lcl|FitnessBrowser__Keio:15734  78 FgELPFLFKVLCAAQPLSIQVHPNKHNSEIGFAKEnaagipmdaaERNYKDPNHKPELVFALTPFLAMNAFREfseivs 156
                                     *************************************************************************999999 PP

                       TIGR00218 140 .Lkriaelh.........eeaerlgkteawviiasdekikeaaeilkealknskeelkekiqrl..iypedvglfkgll 206
                                      L+++a++h         ++aerl++ +a+++++++e++++a +ilk+al++++ e++++i+++  +yped+glf++ll
  lcl|FitnessBrowser__Keio:15734 157 lLQPVAGAHpaiahflqqPDAERLSELFASLLNMQGEEKSRALAILKSALDSQQGEPWQTIRLIseFYPEDSGLFSPLL 235
                                     9999***99****************************************************999*************** PP

                       TIGR00218 207 LnrvklkpgeaiyvrsgtvHAykggdvlEvmanSdnvvragltdkyldvkklvevltveekpeeklkeqkqkegaevlf 285
                                     Ln+vkl+pgea++++++t+HAy++g++lEvmanSdnv+raglt+ky+d+++lv+++++e+kp+++l +q++k+gae++f
  lcl|FitnessBrowser__Keio:15734 236 LNVVKLNPGEAMFLFAETPHAYLQGVALEVMANSDNVLRAGLTPKYIDIPELVANVKFEAKPANQLLTQPVKQGAELDF 314
                                     ******************************************************************************* PP

                       TIGR00218 286 lvpieefavlktdlsekaelksqdsalillvleGdglilsgekklklkkGesfliaakleevtiegedeal 356
                                     ++p+++fa++ +dls+k++++sq+sa+il+++eGd+++++g+++l+lk+Ges++iaa++++vt++g+ ++l
  lcl|FitnessBrowser__Keio:15734 315 PIPVDDFAFSLHDLSDKETTISQQSAAILFCVEGDATLWKGSQQLQLKPGESAFIAANESPVTVKGH-GRL 384
                                     ******************************************************************9.555 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (359 nodes)
Target sequences:                          1  (391 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: 00:00:00.01
# Mc/sec: 11.98
//
[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