GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08260 in Herbaspirillum seropedicae SmR1

Align Branched-chain amino acid ABC transporter,substrate-binding periplasmic component (characterized, see rationale)
to candidate HSERO_RS00870 HSERO_RS00870 ABC transporter substrate-binding protein

Query= uniprot:G8ALJ3
         (366 letters)



>FitnessBrowser__HerbieS:HSERO_RS00870
          Length = 378

 Score =  191 bits (486), Expect = 2e-53
 Identities = 122/364 (33%), Positives = 194/364 (53%), Gaps = 11/364 (3%)

Query: 7   LLVAVAATAMTASVAKAD----IAVATAGPITGQYATFGEQMKKGIEQAVADINAAG-GV 61
           L +  A+ A+  + A A     + +  + P+TG  A+ G+  + G+  A+  +NA    V
Sbjct: 8   LNIIAASLALIPAFAMAQETQVVKIGFSSPLTGPQASAGKDNQGGLMMAIERLNAQPITV 67

Query: 62  LGQKLKLEV--GDDACDPKQAVAVANQLAKAGVKFVAGHFCSGSSIPASQVYAEEGVLQI 119
            G+K+K +V   DD  DPK  VAVA +LA  GVK + G + SG +IPAS+VY + G++ +
Sbjct: 68  GGKKIKFDVIAEDDQADPKSGVAVAQKLADQGVKAIVGPYNSGVTIPASRVYNDAGIV-V 126

Query: 120 SPASTNPKLTEQNLKNVFRVCGRDDQQGQIAGKYLLENYKGKNVAILHDKSAYGKGLADE 179
           +  ++NPK+T+Q    +FRV   D Q G     Y  +  K K VA++ D++AYG+GLA E
Sbjct: 127 ATVASNPKITQQGFATLFRVAASDSQLGGKMALYAAKELKFKRVAVIDDRTAYGQGLAQE 186

Query: 180 TQKALNAGGQKEKIYEAYTAGEKDYSALVSKLKQEAVDVVYVGGYHTEAGLLARQMKDQG 239
             K   A G      +       D++A+++ +K +  D V++GGY  + G + RQMK  G
Sbjct: 187 FIKVAKANGIDVVSTDFTNDKATDFTAILTSIKGKKPDAVFLGGYAPQGGPIKRQMKQLG 246

Query: 240 LNAPIVSGDALVTNEYWAITGPA-GENTMMTFGPDPRE-MPEAKEAVEKFRKAGYEP-EG 296
           ++ P++ GD + + E   + G A GE+   T G    +   E K   ++++K    P E 
Sbjct: 247 VDVPLMGGDGICSPEMGRLGGDAIGESVYCTQGGTMLDKAKEGKVFSDEYQKKYNRPAET 306

Query: 297 YTLYTYAALQIWAEAAKQANSTDSAKIADVLRKNSYNTVIGKIGFDAKGDVTSPAYVWYR 356
           Y +  Y  + + A+A KQANS D  +    L K SY  V G+  FDA  D+       YR
Sbjct: 307 YAVSFYDGMMLIAQAMKQANSVDPKQFGPALAKISYKGVAGQYDFDANHDLKQSPVTVYR 366

Query: 357 WNNG 360
           + +G
Sbjct: 367 FKDG 370


Lambda     K      H
   0.312    0.129    0.366 

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: 391
Number of extensions: 22
Number of successful extensions: 6
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: 366
Length of database: 378
Length adjustment: 30
Effective length of query: 336
Effective length of database: 348
Effective search space:   116928
Effective search space used:   116928
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 49 (23.5 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