GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__azobra:AZOBR_RS30470
          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:

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