Alignments for a candidate for manA in Cronobacter universalis NCTC 9529

GapMind for catabolism of small carbon sources

Alignments for a candidate for manA in Cronobacter universalis NCTC 9529

Align mannose-6-phosphate isomerase (EC 5.3.1.8) (characterized)
to candidate WP_007697503.1 AFK65_RS09110 mannose-6-phosphate isomerase

Query= BRENDA::P25081
         (391 letters)



>NCBI__GCF_001277175.1:WP_007697503.1
          Length = 392

 Score =  644 bits (1660), Expect = 0.0
 Identities = 325/391 (83%), Positives = 349/391 (89%)

Query: 1   MQKLINSVQNYAWGSKTALTELYGIANPQQQPMAELWMGAHPKSSSRITTANGETVSLRD 60
           MQKLINSVQNYAWGSKTALTELYG+ANP+  PMAELWMGAHPKSSS+I  A G+T +LR+
Sbjct: 1   MQKLINSVQNYAWGSKTALTELYGVANPEGLPMAELWMGAHPKSSSKIQDAQGQTRALRE 60

Query: 61  AIEKNKTAMLGEAVANRFGELPFLFKVLCAAQPLSIQVHPNKRNSEIGFAKENAAGIPMD 120
            IE +KTA+LG  VA RFGELPFLFKVLCA QPLSIQVHPNK  SE GFA+ENAAGIP+D
Sbjct: 61  VIEADKTALLGAPVAERFGELPFLFKVLCADQPLSIQVHPNKNASEDGFARENAAGIPLD 120

Query: 121 AAERNYKDPNHKPELVFALTPFLAMNAFREFSDIVSLLQPVAGAHSAIAHFLQVPNAERL 180
           AAERNYKDPNHKPELVFALTPFLAMNAFREFS+IVSLLQPVAGAH+AIAHFL  PNA+RL
Sbjct: 121 AAERNYKDPNHKPELVFALTPFLAMNAFREFSEIVSLLQPVAGAHTAIAHFLAEPNADRL 180

Query: 181 SQLFASLLNMQGEEKSRALAVLKAALNSQQGEPWQTIRVISEYYPDDSGLFSPLLLNVVK 240
             LFA LLNMQGEEKSRALAVLKA + SQQGEPW TIR I+++YPDDSGLFSPLLLNVVK
Sbjct: 181 RDLFAGLLNMQGEEKSRALAVLKATVASQQGEPWDTIRFIAQFYPDDSGLFSPLLLNVVK 240

Query: 241 LNPGEAMFLFAETPHAYLQGVALEVMANSDNVLRAGLTPKYIDIPELVANVKFEPKPAGE 300
           LNPGEAMFLFAETPHAYLQGVALEVMANSDNVLRAGLTPKYIDIPELVANVKF  KPAGE
Sbjct: 241 LNPGEAMFLFAETPHAYLQGVALEVMANSDNVLRAGLTPKYIDIPELVANVKFVAKPAGE 300

Query: 301 LLTAPVKSGAELDFPIPVDDFAFSLHDLALQETSIGQHSAAILFCVEGEAVLRKDEQRLV 360
           LLT P K GA L+FPIPV+DFAFSLHDL  Q  S+ Q SAAILFCVEGEAVL K ++RL 
Sbjct: 301 LLTQPEKDGAALEFPIPVEDFAFSLHDLHSQPQSLAQESAAILFCVEGEAVLSKGDERLS 360

Query: 361 LKPGESAFIGADESPVNASGTGRLARVYNKL 391
           LKPGESAFI A+ESPV+ SG GRLARVYNKL
Sbjct: 361 LKPGESAFIAANESPVSVSGVGRLARVYNKL 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: 616
Number of extensions: 19
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 WP_007697503.1 AFK65_RS09110 (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.1997870.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   7.5e-129  415.9   0.0   8.4e-129  415.7   0.0    1.0  1  NCBI__GCF_001277175.1:WP_007697503.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001277175.1:WP_007697503.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  415.7   0.0  8.4e-129  8.4e-129       2     354 ..       3     382 ..       1     387 [. 0.96

  Alignments for each domain:
  == domain 1  score: 415.7 bits;  conditional E-value: 8.4e-129
                             TIGR00218   2 kflfrvqknlkerdWGkgtaladllgysip.skqtaElWagaHkkgsSkvqng..kkvsLrdliekhksellG 71 
                                           k++++v    ++++WG++tal++l+g ++p + ++aElW+gaH+k+sSk+q +  +   Lr++ie +k +llG
  NCBI__GCF_001277175.1:WP_007697503.1   3 KLINSV----QNYAWGSKTALTELYGVANPeGLPMAELWMGAHPKSSSKIQDAqgQTRALREVIEADKTALLG 71 
                                           345555....559****************94556*****************96569999************** PP

                             TIGR00218  72 kaeadrf.elPlLvkvLsaekplsiqvHPdkalakigyake..........krnYkDknhkpelvialtdfea 133
                                             +a+rf elP+L+kvL+a++plsiqvHP+k+ ++ g+a+e          +rnYkD+nhkpelv+alt+f+a
  NCBI__GCF_001277175.1:WP_007697503.1  72 APVAERFgELPFLFKVLCADQPLSIQVHPNKNASEDGFAREnaagipldaaERNYKDPNHKPELVFALTPFLA 144
                                           ************************************************************************* PP

                             TIGR00218 134 lkgfkp.......Lkriaelh.........eeaerlgkteawviiasdekikeaaeilkealknskeelkeki 190
                                           +++f++       L+++a++h         ++a+rl   +a ++++++e++++a ++lk  +++++ e++ +i
  NCBI__GCF_001277175.1:WP_007697503.1 145 MNAFREfseivslLQPVAGAHtaiahflaePNADRLRDLFAGLLNMQGEEKSRALAVLKATVASQQGEPWDTI 217
                                           ******999999999999999**************************************************** PP

                             TIGR00218 191 qrl..iypedvglfkgllLnrvklkpgeaiyvrsgtvHAykggdvlEvmanSdnvvragltdkyldvkklvev 261
                                           + +  +yp+d+glf++llLn+vkl+pgea++++++t+HAy++g++lEvmanSdnv+raglt+ky+d+++lv++
  NCBI__GCF_001277175.1:WP_007697503.1 218 RFIaqFYPDDSGLFSPLLLNVVKLNPGEAMFLFAETPHAYLQGVALEVMANSDNVLRAGLTPKYIDIPELVAN 290
                                           999*9******************************************************************** PP

                             TIGR00218 262 ltveekpeeklkeqkqkegaevlflvpieefavlktdlsekaelksqdsalillvleGdglilsgekklklkk 334
                                           +++ +kp+ +l +q++k ga + f++p+e+fa++ +dl  + +   q+sa+il+++eG++++ +g+++l lk+
  NCBI__GCF_001277175.1:WP_007697503.1 291 VKFVAKPAGELLTQPEKDGAALEFPIPVEDFAFSLHDLHSQPQSLAQESAAILFCVEGEAVLSKGDERLSLKP 363
                                           ************************************************************************* PP

                             TIGR00218 335 Gesfliaakleevtiegede 354
                                           Ges++iaa++++v + g  +
  NCBI__GCF_001277175.1:WP_007697503.1 364 GESAFIAANESPVSVSGV-G 382
                                           ***************997.4 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 17.29
//
[ok]

This GapMind analysis is from Sep 24 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