GapMind for catabolism of small carbon sources

 

Alignments for a candidate for opuBA in Herbaspirillum seropedicae SmR1

Align BilEA aka OpuBA protein, component of A proline/glycine betaine uptake system. Also reported to be a bile exclusion system that exports oxgall and other bile compounds, BilEA/EB or OpuBA/BB (required for normal virulence) (characterized)
to candidate HSERO_RS03005 HSERO_RS03005 ABC transporter ATP-binding protein

Query= TCDB::Q93A35
         (328 letters)



>FitnessBrowser__HerbieS:HSERO_RS03005
          Length = 361

 Score =  178 bits (451), Expect = 2e-49
 Identities = 99/240 (41%), Positives = 152/240 (63%), Gaps = 6/240 (2%)

Query: 2   IRFDNVSKKYSDDKTAAVNNVTLDIKDGEFFVFIGPSGCGKTTTLKMINRL-IPLTTGTI 60
           IR    +K +++  T A+  + L I  GE  V +GPSGCGKTTTL+MI  L  P   G +
Sbjct: 10  IRLSQCAKSFANG-TRALQPLDLQIHPGETLVLLGPSGCGKTTTLRMIAGLEFPDEGGRV 68

Query: 61  YINEKRISDYDIHELRWDIGYVLQQIALFPHMTIEENIAIVPELKKWSKEKIHDRITELL 120
              E+ ++   I +    +G V Q  ALFP+M++ ENIA   +++K +  +  +R+  LL
Sbjct: 69  LFGEEDVTMLPIEKR--GVGMVFQNYALFPNMSVGENIAYGMKIRKIAAGERAERVERLL 126

Query: 121 DSVGLDPESYRHRKPAELSGGEQQRVGVVRALAADPGIILMDEPFSALDPISRQRLQQDI 180
           + V L  +   HR+  +LSGG++QRV + RALA +P ++L+DEP +ALD   R+ ++ D+
Sbjct: 127 EMVHL--QGLSHRRVDQLSGGQKQRVALARALAMEPRVLLLDEPLTALDAKLREAVRSDL 184

Query: 181 SALQKKIKKTIVFVTHDMQEALALGDRICVMQGGEIVQVATPQEIMKNPENDFVKDFLAS 240
           + L + +  T ++VTHD  EA+ALGDRI VM+ G+I Q+ TPQEI  +P NDFV +F+ +
Sbjct: 185 NKLLRSLGITAIYVTHDQGEAMALGDRIVVMERGKISQIGTPQEIYYHPANDFVAEFIGA 244


Lambda     K      H
   0.318    0.136    0.386 

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: 265
Number of extensions: 10
Number of successful extensions: 3
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: 328
Length of database: 361
Length adjustment: 29
Effective length of query: 299
Effective length of database: 332
Effective search space:    99268
Effective search space used:    99268
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: 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