Aligments for a candidate for nagF in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Aligments 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)



>lcl|FitnessBrowser__azobra:AZOBR_RS18900 AZOBR_RS18900 peptidase
          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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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, 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

GapMind for catabolism of small carbon sources