Alignments for a candidate for arcC in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for arcC in Klebsiella michiganensis M5al

Align carbamate kinase (EC 2.7.2.2) (characterized)
to candidate BWI76_RS17520 BWI76_RS17520 carbamate kinase

Query= BRENDA::P0A2X7
         (310 letters)



>FitnessBrowser__Koxy:BWI76_RS17520
          Length = 310

 Score =  287 bits (734), Expect = 3e-82
 Identities = 153/296 (51%), Positives = 204/296 (68%), Gaps = 7/296 (2%)

Query: 1   MGKKMVVALGGNAILSNDASAHAQQQALVQTSAYLVHLIKQGHRLIVSHGNGPQVG--NL 58
           M KK+V+ALGGNA L +D +   Q QA+  T+  +V LI  GH+++V+HGNGPQVG  N 
Sbjct: 1   MSKKIVLALGGNA-LGDDLAG--QMQAVRHTARTIVDLIALGHQVVVTHGNGPQVGMINQ 57

Query: 59  LLQQQAADSEKNPAMPLDTCVAMTQGSIGYWLSNALNQELNKAGIKKQVATVLTQVVVDP 118
             +  A      P +P+  CVA++QG IGY L NA+ +EL    +   VAT++TQV VD 
Sbjct: 58  AFEAAAKTEAHTPMLPMSVCVALSQGYIGYDLQNAIREELLSRQLDIPVATLITQVEVDA 117

Query: 119 ADEAFKNPTKPIGPFLTEAEAKEAMQAGAIFKEDAGRGWRKVVPSPKPIDIHEAETINTL 178
            DEAF NPTKPIG F ++ EA++  Q G I KEDAGRG+R+VV SPKP+DI E +T+  L
Sbjct: 118 NDEAFLNPTKPIGSFFSKEEAEKLSQNGYIMKEDAGRGYRRVVASPKPVDIIEKQTVKAL 177

Query: 179 IKNDIITISCGGGGIPVV--GQELKGVEAVIDKDFASEKLAELVDADALVILTGVDYVCI 236
           + +  + I+ GGGGIPV+  G  L+G  AVIDKD+AS KLAE +DAD L+ILT V+ V I
Sbjct: 178 MDDCHVVITVGGGGIPVIREGNHLRGASAVIDKDWASAKLAETIDADLLIILTAVEKVAI 237

Query: 237 NYGKPDEKQLTNVTVAELEEYKQAGHFAPGSMLPKIEAAIQFVESQPNKQAIITSL 292
           N+GKP E+ L N+++ + E +   GHFA GSMLPK+EAA  F  S+P +QA+IT L
Sbjct: 238 NFGKPGEQWLDNLSLRDAERFIAEGHFAKGSMLPKVEAAAAFARSRPGRQALITML 293


Lambda     K      H
   0.313    0.131    0.368 

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: 272
Number of extensions: 13
Number of successful extensions: 4
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: 310
Length of database: 310
Length adjustment: 27
Effective length of query: 283
Effective length of database: 283
Effective search space:    80089
Effective search space used:    80089
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 48 (23.1 bits)

Align candidate BWI76_RS17520 BWI76_RS17520 (carbamate kinase)
to HMM TIGR00746 (arcC: carbamate kinase (EC 2.7.2.2))

# 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/TIGR00746.hmm
# target sequence database:        /tmp/gapView.996.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00746  [M=309]
Accession:   TIGR00746
Description: arcC: carbamate kinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   1.9e-117  377.6   1.0   2.2e-117  377.5   1.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS17520  BWI76_RS17520 carbamate kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS17520  BWI76_RS17520 carbamate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  377.5   1.0  2.2e-117  2.2e-117       1     308 [.       3     309 ..       3     310 .] 0.96

  Alignments for each domain:
  == domain 1  score: 377.5 bits;  conditional E-value: 2.2e-117
                               TIGR00746   1 kkvvvaLGGnallqrgekasaeeqrknvekaakqlvklakrgyelvithGngPqvGalllqneaads.... 67 
                                             kk+v+aLGGnal       +   q+++v+++a+++v+l++ g+++v+thGngPqvG +    eaa++    
  lcl|FitnessBrowser__Koxy:BWI76_RS17520   3 KKIVLALGGNALG-----DDLAGQMQAVRHTARTIVDLIALGHQVVVTHGNGPQVGMINQAFEAAAKteah 68 
                                             79**********8.....677899**********************************8777776665677 PP

                               TIGR00746  68 vpakPldvlgaesqgliGYllqqalkeelakeglekkvatvltqvivdekDeaFqnPtkpigpfydeeeak 138
                                             +p  P+ v++a sqg iGY lq+a++eel  ++l  +vat++tqv+vd++DeaF nPtkpig f+++eea+
  lcl|FitnessBrowser__Koxy:BWI76_RS17520  69 TPMLPMSVCVALSQGYIGYDLQNAIREELLSRQLDIPVATLITQVEVDANDEAFLNPTKPIGSFFSKEEAE 139
                                             8889******************************************************************* PP

                               TIGR00746 139 rlaaekgailkedagrgwRrvvpsPkPkeiveaeviktLvekgvivissgGGGvPvvkdgkelkGveaviD 209
                                             +l  ++g+i+kedagrg+Rrvv+sPkP++i+e +++k L+++ ++vi+ gGGG+Pv+++g++l+G  aviD
  lcl|FitnessBrowser__Koxy:BWI76_RS17520 140 KL-SQNGYIMKEDAGRGYRRVVASPKPVDIIEKQTVKALMDDCHVVITVGGGGIPVIREGNHLRGASAVID 209
                                             65.578***************************************************************** PP

                               TIGR00746 210 kDlasekLaeevnaDilviltdvdavyvnygkpdekkleevkveeleelakdgefaaGsmgPkveaaiefv 280
                                             kD as+kLae+++aD l+ilt+v++v++n+gkp e++l ++++ ++e+++++g+fa+Gsm+Pkveaa  f+
  lcl|FitnessBrowser__Koxy:BWI76_RS17520 210 KDWASAKLAETIDADLLIILTAVEKVAINFGKPGEQWLDNLSLRDAERFIAEGHFAKGSMLPKVEAAAAFA 280
                                             *********************************************************************** PP

                               TIGR00746 281 esrgk.kaiitslekivealegkaGtvvv 308
                                             +sr+  +a+it l+k++e +egk+Gt+++
  lcl|FitnessBrowser__Koxy:BWI76_RS17520 281 RSRPGrQALITMLSKAKEGIEGKTGTIIS 309
                                             **9877*********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (309 nodes)
Target sequences:                          1  (310 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: 9.95
//
[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