Alignments for a candidate for fba in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for fba in Azospirillum brasilense Sp245

Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate AZOBR_RS30885 AZOBR_RS30885 fructose-bisphosphate aldolase

Query= BRENDA::P0AB71
         (359 letters)



>FitnessBrowser__azobra:AZOBR_RS30885
          Length = 359

 Score =  370 bits (951), Expect = e-107
 Identities = 192/351 (54%), Positives = 249/351 (70%), Gaps = 8/351 (2%)

Query: 8   VKPGVITGDDVQKVFQVAKENNFALPAVNCVGTDSINAVLETAAKVKAPVIVQFSNGGAS 67
           +KPGV+TG+D + +    ++  +ALPAVN VGT+ INAVLE AAK ++ VIVQ SNGGA 
Sbjct: 7   LKPGVVTGEDYRALIAACQDGGYALPAVNVVGTNGINAVLEAAAKNRSDVIVQLSNGGAR 66

Query: 68  FIAGKGVKSDVPQGAAILGAISGAHHVHQMAEHYGVPVILHTDHCAKKLLPWIDGLLDAG 127
           F AG+G+K  +   A ILGA+S A HVH +AE YGV V+LHTDH  K L+PW++G++D G
Sbjct: 67  FYAGEGMKDALQ--ARILGAVSAAQHVHLLAEQYGVCVVLHTDHANKGLIPWVEGMIDHG 124

Query: 128 EKHFAATGKPLFSSHMIDLSEESLQENIEICSKYLERMSKIGMTLEIELGCTGGEEDGVD 187
           E+HF  TG+PLFSSHM+DLSEESL  N+  C++ L+R++ +GM+LEIELG TGGEEDG+ 
Sbjct: 125 EEHFRRTGRPLFSSHMLDLSEESLDFNLSECARVLKRLAPLGMSLEIELGVTGGEEDGIG 184

Query: 188 NSHMDA---SALYTQPEDVDYAYTELSKISPRFTIAASFGNVHGVYKPGNVVLTPTILRD 244
           +  +DA   + LYTQPEDV  AY ELS I   F++AASFGNVHGVY PGNV L P IL  
Sbjct: 185 SEDLDAANNAHLYTQPEDVLRAYEELSPIG-HFSVAASFGNVHGVYAPGNVKLRPEILGA 243

Query: 245 SQEYVSKKHNLPHNSLNFVFHGGSGSTAQEIKDSVSYGVVKMNIDTDTQWATWEGVLNYY 304
           SQ  V+++H      L  VFHGGSGS  ++I  +V +GV KMNIDTDTQ+A  E +  + 
Sbjct: 244 SQALVAERHGGGAKPLALVFHGGSGSEKEKIAQAVGFGVFKMNIDTDTQFAFAESIGGFV 303

Query: 305 KANEAYLQGQLGNPKGEDQPNKKYYDPRVWLRAGQTSMIARLEKAFQELNA 355
             NEA  + Q+    G  +P KK YDPR WLR G+  M+ RL++AF +L A
Sbjct: 304 LENEAAFRHQIDPQSG--KPLKKLYDPRKWLRLGEQGMVRRLDEAFADLGA 352


Lambda     K      H
   0.316    0.133    0.392 

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: 395
Number of extensions: 17
Number of successful extensions: 5
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: 359
Length of database: 359
Length adjustment: 29
Effective length of query: 330
Effective length of database: 330
Effective search space:   108900
Effective search space used:   108900
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: 49 (23.5 bits)

Align candidate AZOBR_RS30885 AZOBR_RS30885 (fructose-bisphosphate aldolase)
to HMM TIGR01520 (fbaA: fructose-bisphosphate aldolase, class II (EC 4.1.2.13))

# 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/TIGR01520.hmm
# target sequence database:        /tmp/gapView.8630.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01520  [M=357]
Accession:   TIGR01520
Description: FruBisAldo_II_A: fructose-bisphosphate aldolase, class II
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.7e-139  450.1   0.0   3.4e-139  449.7   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS30885  AZOBR_RS30885 fructose-bisphosph


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS30885  AZOBR_RS30885 fructose-bisphosphate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  449.7   0.0  3.4e-139  3.4e-139       4     356 ..       6     355 ..       4     356 .. 0.96

  Alignments for each domain:
  == domain 1  score: 449.7 bits;  conditional E-value: 3.4e-139
                                 TIGR01520   4 klktgvilgedvaklfevakeekfaiPainvvssetvnaaleaardakspiilqfsnggaafiaGkGvk 72 
                                                lk+gv++ged++ l+  +++  +a+Pa+nvv+++ +na+leaa++ +s++i+q+sngga f+aG G+k
  lcl|FitnessBrowser__azobra:AZOBR_RS30885   6 RLKPGVVTGEDYRALIAACQDGGYALPAVNVVGTNGINAVLEAAAKNRSDVIVQLSNGGARFYAGEGMK 74 
                                               5799***************************************************************** PP

                                 TIGR01520  73 deaekaasiaGaiaaaeyvrsiaekygvpvvlhtdhCakkllpyvdglleadekyfkkegkPlfsshml 141
                                               d a +a  i Ga++aa++v+ +ae+ygv vvlhtdh  k l+p+v+g+++++e++f+++g+Plfsshml
  lcl|FitnessBrowser__azobra:AZOBR_RS30885  75 D-ALQA-RILGAVSAAQHVHLLAEQYGVCVVLHTDHANKGLIPWVEGMIDHGEEHFRRTGRPLFSSHML 141
                                               9.5566.7************************************************************* PP

                                 TIGR01520 142 dlseepieenieiakkylkrmakiklileieiGitGGeedGvdneead...keelytkPedvekvyeel 207
                                               dlsee+++ n++ + + lkr+a++ + leie+G+tGGeedG+  e+ d   +++lyt+Pedv ++yeel
  lcl|FitnessBrowser__azobra:AZOBR_RS30885 142 DLSEESLDFNLSECARVLKRLAPLGMSLEIELGVTGGEEDGIGSEDLDaanNAHLYTQPEDVLRAYEEL 210
                                               ******************************************998866222678*************** PP

                                 TIGR01520 208 skispkfsiaaafGnvhGvykpGnvklrPdiladgqeyvaeklglkeakplsfvfhGGsGstkeeikea 276
                                               s+i ++fs+aa+fGnvhGvy+pGnvklrP+il  +q+ vae++g   akpl +vfhGGsGs ke i +a
  lcl|FitnessBrowser__azobra:AZOBR_RS30885 211 SPI-GHFSVAASFGNVHGVYAPGNVKLRPEILGASQALVAERHGGG-AKPLALVFHGGSGSEKEKIAQA 277
                                               **9.79**************************************99.9********************* PP

                                 TIGR01520 277 lsyGvvkvnvdtdtqyaalegildyvlknedylqsqvGnpkgeekpnkkvydPrvwlreaeksmkarve 345
                                               + +Gv k+n+dtdtq+a+ e+i ++vl+ne+  ++q+  p +  kp kk ydPr wlr +e+ m  r+ 
  lcl|FitnessBrowser__azobra:AZOBR_RS30885 278 VGFGVFKMNIDTDTQFAFAESIGGFVLENEAAFRHQID-P-QSGKPLKKLYDPRKWLRLGEQGMVRRLD 344
                                               ************************************98.4.5679************************ PP

                                 TIGR01520 346 kaleelnaink 356
                                               +a+ +l a++k
  lcl|FitnessBrowser__azobra:AZOBR_RS30885 345 EAFADLGAAGK 355
                                               ****9988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (357 nodes)
Target sequences:                          1  (359 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: 11.77
//
[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