GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagF in Azospirillum brasilense Sp245

Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate AZOBR_RS18900 AZOBR_RS18900 peptidase

Query= reanno::pseudo3_N2E3:AO353_04460
         (838 letters)



>FitnessBrowser__azobra:AZOBR_RS18900
          Length = 766

 Score =  269 bits (687), Expect = 5e-76
 Identities = 195/586 (33%), Positives = 279/586 (47%), Gaps = 24/586 (4%)

Query: 242 AALQALLNALSTAVNDDSHAAAPTPIAQRTRTAEAGVLNGVCAAPGLVGGPLFQLAAIPL 301
           A + A L A    VN    A+   P     R      L+G   A GL  G    LA I  
Sbjct: 165 AMVVAELVAQGELVNPQEVASTGDPALLPAR------LSGTSLASGLAMG----LAVIHR 214

Query: 302 PEDTGKH----NAEEQLQALDRALEQVRSEIRETLSHAKKHKHTEEEQIFAAHLALLEDP 357
           P+ T +     +AE +L  L+ A+  + S I + L+ A     +E + I   +    ED 
Sbjct: 215 PQLTIRQMVSEDAESELARLNAAIATMHSAIDDLLNAAALAGLSEPKDILETYRMFAEDR 274

Query: 358 ALLEAAIQSIDQGSAATHAWSQSIEAQCEVLQQLGNPLLAERANDLRDLRQRVLRALLGQ 417
             L    ++I  G  A  A  Q        +  L +P + ER  DL DL  R+L+ L G+
Sbjct: 275 GWLSRIREAIRMGLTAEGAVQQVQNDTRARMSHLTDPYIRERLLDLEDLTNRLLQHLAGR 334

Query: 418 DWHYD---VPAGAIVAAHELTPSDLLQLSQQGVAGLCMAEGGATSHVAILARGKGLPCLV 474
               D   +P   ++ A  + P++LL   Q+ + G+ + EG  +SHV I+AR   +P + 
Sbjct: 335 KSEADGGTLPEDIVLVARSMGPAELLDYDQRRLRGVILEEGSPSSHVCIVARALNIPVVQ 394

Query: 475 ALSASLLQQPQGQSVVLDADGGRLELTPDSQRLEQVAQAQREHLQRRERQQAQAHTPAHT 534
           A  A    +P    V++D D G+  + P        A+A     ++ +  +A    P+ T
Sbjct: 395 APDALNRIEPL-DPVIVDGDHGQAFVRPAEDIQMAFAEAVALRARKEQMYEAIRAQPSVT 453

Query: 535 RDGLRIEVAANVASSNEAADALKGGADGVGLLRTEFLFVDRQTAPDEQEQRQAYQAVLDA 594
           RDG+ I +  N     +       GA+G+GL RTE  F+ R T PD   Q   Y  +LD 
Sbjct: 454 RDGVPISIQLNCGLLIDLPHLKASGAEGIGLYRTEIPFMVRSTYPDVHAQTDLYSRILDQ 513

Query: 595 MGDKSVIIRTIDVGGDKQLDYLPL-PAEANPVLGLRGIRMAQVRPELLDQQLRALLQVSP 653
             DK V+ RT+DVGGDK L Y+     E NP LG R IR+    P LL QQLRALL+ S 
Sbjct: 514 TDDKPVVFRTLDVGGDKMLPYIAASEGEENPALGWRAIRIGLDHPSLLRQQLRALLRASA 573

Query: 654 LQRCRILLPMVTEVDELLYIRQRLDALCAEL-----ALTQRLELGVMIEVPAAALLAEQL 708
            +   ++ PM+ EV E    R+ LD     L         R+ +G MIEVPA       L
Sbjct: 574 GRPLSVMFPMIAEVAEFDAARRLLDLEINRLKGQGGEPPSRVRVGTMIEVPALLWQLPAL 633

Query: 709 AEHADFLSIGTNDLSQYTLAMDRDHAGLAARVDALHPALLRLIAQTCIGAAKHQRWVGVC 768
               DFLS+G+NDL+QY  A DR +   + R D L PA++ L+ +           V +C
Sbjct: 634 LPRVDFLSVGSNDLTQYIFASDRGNPRTSGRYDPLSPAMMSLLRRLVEACGDAGVPVSIC 693

Query: 769 GALASDPLATPVLIGLGISELSVSPPQVGEIKERVRQLDAADCRRF 814
           G +A  PL    LIG+G   LS+SPP VG +K  +R LD A  R++
Sbjct: 694 GEMAGRPLDAMALIGIGFRTLSMSPPSVGPVKTMLRSLDVAVLRQY 739


Lambda     K      H
   0.318    0.133    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: 1359
Number of extensions: 69
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: 838
Length of database: 766
Length adjustment: 41
Effective length of query: 797
Effective length of database: 725
Effective search space:   577825
Effective search space used:   577825
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 (21.7 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