Alignments for a candidate for manA in Tatumella morbirosei LMG 23360

GapMind for catabolism of small carbon sources

Alignments for a candidate for manA in Tatumella morbirosei LMG 23360

Align mannose-6-phosphate isomerase (EC 5.3.1.8) (characterized)
to candidate WP_038018188.1 HA49_RS13120 mannose-6-phosphate isomerase

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



>NCBI__GCF_000757425.2:WP_038018188.1
          Length = 391

 Score =  449 bits (1154), Expect = e-131
 Identities = 228/385 (59%), Positives = 275/385 (71%), Gaps = 1/385 (0%)

Query: 1   MQKLINSVQNYAWGSKTALTELYGMENPSSQPMAELWMGAHPKSSSRVQNAAGDIVSLRD 60
           M KLIN++Q+Y WGSKT LTELYG+ENP + PMAELWMGAHP + SRV   AG  VSL +
Sbjct: 1   MDKLINTIQHYDWGSKTTLTELYGIENPENLPMAELWMGAHPDAPSRVV-VAGQPVSLAE 59

Query: 61  VIESDKSTLLGEAVAKRFGELPFLFKVLCAAQPLSIQVHPNKHNSEIGFAKENAAGIPMD 120
           +I      LLGE VA+RF  LP+LFKVLCAA PLS+QVHP+K  +E GF +EN AGIP+ 
Sbjct: 60  LIRQQPQQLLGEKVARRFSGLPYLFKVLCAAGPLSVQVHPDKQAAEQGFQRENQAGIPLS 119

Query: 121 AAERNYKDPNHKPELVFALTPFLAMNAFREFSEIVSLLQPVAGAHPAIAHFLQQPDAERL 180
           +  RNYKD NHKPELV+ALTPF AMN FR   +I  LL+P+ GAHP I  F+ +P+   L
Sbjct: 120 SPLRNYKDNNHKPELVYALTPFRAMNGFRPPQQIAGLLEPLVGAHPQIGAFVARPEMAGL 179

Query: 181 SELFASLLNMQGEEKSRALAILKSALDSQQGEPWQTIRLISEFYPEDSGLFSPLLLNVVK 240
             LFA LL++QG+E + AL  L        GE WQT+R +   YP D G F PLLLNVV 
Sbjct: 180 KALFAVLLSLQGDEAALALKWLAEVSAGLPGETWQTVRSLQHSYPGDMGQFMPLLLNVVV 239

Query: 241 LNPGEAMFLFAETPHAYLQGVALEVMANSDNVLRAGLTPKYIDIPELVANVKFEAKPANQ 300
           L PG+AMFLFA+TPHAYLQG  LE+MANS+NVLRAGLT K+IDIPEL+ NV+F + PA Q
Sbjct: 240 LQPGQAMFLFAKTPHAYLQGSGLEIMANSNNVLRAGLTAKHIDIPELLDNVEFVSHPAEQ 299

Query: 301 LLTQPVKQGAELDFPIPVDDFAFSLHDLSDKETTISQQSAAILFCVEGDATLWKGSQQLQ 360
           LLTQPV    E+ FP+PVDDF+F++H L      +S     I+ C+EG A      QQL 
Sbjct: 300 LLTQPVVSQHEISFPVPVDDFSFAVHQLQPTAQALSWPGPRIILCLEGTARCECSGQQLT 359

Query: 361 LKPGESAFIAANESPVTVKGHGRLA 385
           L+PGESAFI ANE P+TV G GRLA
Sbjct: 360 LRPGESAFIPANEGPLTVSGQGRLA 384


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: 512
Number of extensions: 22
Number of successful extensions: 2
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 WP_038018188.1 HA49_RS13120 (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.613432.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.6e-107  345.0   0.0   3.1e-107  344.8   0.0    1.0  1  NCBI__GCF_000757425.2:WP_038018188.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000757425.2:WP_038018188.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  344.8   0.0  3.1e-107  3.1e-107       7     353 ..       4     381 ..       1     385 [. 0.96

  Alignments for each domain:
  == domain 1  score: 344.8 bits;  conditional E-value: 3.1e-107
                             TIGR00218   7 vqknlkerdWGkgtaladllgysipskq.taElWagaHkkgsSkvqn.gkkvsLrdliekhksellGkaeadr 77 
                                           + + ++++dWG++t l++l+g ++p +  +aElW+gaH+  +S+v + g+ vsL +li +++++llG+++a r
  NCBI__GCF_000757425.2:WP_038018188.1   4 LINTIQHYDWGSKTTLTELYGIENPENLpMAELWMGAHPDAPSRVVVaGQPVSLAELIRQQPQQLLGEKVARR 76 
                                           5677999******************9867******************66************************ PP

                             TIGR00218  78 f.elPlLvkvLsaekplsiqvHPdkalakigyake..........krnYkDknhkpelvialtdfealkgfkp 139
                                           f  lP L+kvL+a+ pls+qvHPdk+ a+ g+++e           rnYkD+nhkpelv+alt+f a++gf+p
  NCBI__GCF_000757425.2:WP_038018188.1  77 FsGLPYLFKVLCAAGPLSVQVHPDKQAAEQGFQREnqagiplsspLRNYKDNNHKPELVYALTPFRAMNGFRP 149
                                           *99*****************************************99*************************** PP

                             TIGR00218 140 Lkriaelh................eeaerlgkteawviiasdekikeaaeilkealknskeelkekiqrl..i 194
                                            ++ia+l                 +e   l++ +a ++  ++++   a + l e ++    e +++++ l   
  NCBI__GCF_000757425.2:WP_038018188.1 150 PQQIAGLLeplvgahpqigafvarPEMAGLKALFAVLLSLQGDEAALALKWLAEVSAGLPGETWQTVRSLqhS 222
                                           88888888888888899999998855555**************************************999889 PP

                             TIGR00218 195 ypedvglfkgllLnrvklkpgeaiyvrsgtvHAykggdvlEvmanSdnvvragltdkyldvkklvevltveek 267
                                           yp d g+f +llLn+v l+pg a++++++t+HAy++g  lE+manS+nv+raglt k +d+++l+ ++++ ++
  NCBI__GCF_000757425.2:WP_038018188.1 223 YPGDMGQFMPLLLNVVVLQPGQAMFLFAKTPHAYLQGSGLEIMANSNNVLRAGLTAKHIDIPELLDNVEFVSH 295
                                           ************************************************************************* PP

                             TIGR00218 268 peeklkeqkqkegaevlflvpieefavlktdlsekaelksqdsalillvleGdglilsgekklklkkGesfli 340
                                           p+e+l +q++ ++ e+ f+vp+++f++  ++l+ +a+  s  ++ i+l+leG +++   +++l l++Ges++i
  NCBI__GCF_000757425.2:WP_038018188.1 296 PAEQLLTQPVVSQHEISFPVPVDDFSFAVHQLQPTAQALSWPGPRIILCLEGTARCECSGQQLTLRPGESAFI 368
                                           ************************************************************************* PP

                             TIGR00218 341 aakleevtieged 353
                                           +a+++++t+ g++
  NCBI__GCF_000757425.2:WP_038018188.1 369 PANEGPLTVSGQG 381
                                           **********984 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 15.20
//
[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