GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fruI in Azospirillum brasilense Sp245

Align Fructose-specific PTS system, I, HPr, and IIA components (characterized)
to candidate AZOBR_RS30470 AZOBR_RS30470 phosphoenolpyruvate-protein phosphotransferase

Query= reanno::pseudo3_N2E3:AO353_05485
         (953 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS30470 AZOBR_RS30470
           phosphoenolpyruvate-protein phosphotransferase
          Length = 590

 Score =  367 bits (943), Expect = e-106
 Identities = 230/581 (39%), Positives = 336/581 (57%), Gaps = 23/581 (3%)

Query: 393 VVAPASGCVIQAVAAAPGIAIGPAHIQVLQAI---DYPLRGESTAIERERLKTSLADVRR 449
           V A   G  ++ +  +PGIAIGPAH+    AI   +Y L  +    E  R   +    RR
Sbjct: 5   VPAAGQGRSLRGLGVSPGIAIGPAHVVESGAIRVPEYTLTADQVEAEAARFADACGKARR 64

Query: 450 DIEGL------IQRSKAKAIREIFITHQEMLDDPELTDEVDTRLKQG-ESAEAAWMAVID 502
            I  L      +  S ++ I  +   H  M+ +  LT  V+ R++Q   +AEAA  A I 
Sbjct: 65  QIRKLKAKALVLPGSASEEIGFLLDAHLAMVTNSRLTRGVERRIQQELVNAEAAVQAEIA 124

Query: 503 AAARQQESLQDALLAERAADLRDIGRRVLAQLCGIETP--SEPDQPYILVMDEVGPSDVA 560
             A+   S++D+ LA R AD+R++GRR++  L   E    S  +   +++ +E+ P+D A
Sbjct: 125 TIAQTFASMEDSYLAGRIADVREVGRRLIRNLMRHEYQAFSMLNPGAVILAEELTPADTA 184

Query: 561 RLDPTRVAGILTARGGATAHSAIVARALGIPALVGAGAAVLRLASGTPLLLDGQRGRLHV 620
            LDP RVAG  T  GGA  H+AI+AR+LGIPA++G G  +  L +G  +++DG +GR+ +
Sbjct: 185 LLDPRRVAGFATVLGGAEGHTAIMARSLGIPAVLGVGGLLAGLKNGITVIVDGVQGRVII 244

Query: 621 DADAATLQRAAEERDNREQRLQAAAAQRHQPALTTDGHAVEVFANIGESAGVVSAVEQGA 680
           D     L+   + R  RE+  +     R  PA+T D  AV + AN+     +  A+E GA
Sbjct: 245 DPTPEVLEDYRQRRAEREREREQLKGLRKLPAVTRDNTAVTLQANLELPRDLDHALENGA 304

Query: 681 EGIGLLRTELIFMAHQQAPDEATQEVEYRRVLDGLAGRPLVVRTLDVGGDKPLPYWPIAK 740
           +GIGLLRTE +FM   Q PDE  Q    R +++G+ GR +  RT+DVGG+K L  W   +
Sbjct: 305 QGIGLLRTEFLFMNRDQLPDEDEQYTVLRSIVEGMGGRTVTARTMDVGGEK-LAGWMAGR 363

Query: 741 ---EENPFLGVRGIRLTLQRPQIMEAQLRALLRAADNRPLRIMFPMVGSVDEWRQARDM- 796
                NP LG+R +RL L+ P+++E QL A+LRA  + PLRI+ PM+ SV E ++ R+M 
Sbjct: 364 YGEPANPALGLRAVRLGLREPKLLETQLAAMLRAGVHGPLRILLPMICSVAEVQRVREMM 423

Query: 797 ---TERLRLE-IPVAD--LQLGIMIEVPSAALLAPVLAKEVDFFSVGTNDLTQYTLAIDR 850
                RLR   +P+AD    +G+M+EVP AAL A  LA   DFFS+GTNDLTQYTLAIDR
Sbjct: 424 GQVARRLRRRGVPIADPLPPVGVMVEVPGAALSADALAYAADFFSIGTNDLTQYTLAIDR 483

Query: 851 GHPTLSAQADGLHPAVLQLIDITVRAAHAHGKWVGVCGELAADPLAVPVLVGLGVDELSV 910
           G   +++  D LHPAVL+LI  T+ AA      V VCGE+A D     +L+GLGV +LS+
Sbjct: 484 GDEQVASLYDPLHPAVLRLIQFTIEAALRARIPVSVCGEIAGDSRYTALLLGLGVRDLSM 543

Query: 911 SARSIGEVKARVRELSLAQVKHLAQLALAVGSANEVRALVE 951
              +I  VK R+R+L L +    A++ +    +  + AL++
Sbjct: 544 VPPAIPLVKRRIRKLDLQEATRRARVIMDQSDSGRIAALLD 584


Lambda     K      H
   0.319    0.135    0.383 

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: 1067
Number of extensions: 46
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: 953
Length of database: 590
Length adjustment: 40
Effective length of query: 913
Effective length of database: 550
Effective search space:   502150
Effective search space used:   502150
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 bits)

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:

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:

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:

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, or view the source code.

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