GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natH in Marinobacter adhaerens HP15

Align NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate GFF2244 HP15_2194 amino acid ABC transporter, permease protein

Query= TCDB::Q8YPM7
         (381 letters)



>FitnessBrowser__Marino:GFF2244
          Length = 362

 Score =  245 bits (625), Expect = 2e-69
 Identities = 141/392 (35%), Positives = 210/392 (53%), Gaps = 70/392 (17%)

Query: 6   WLRKNLFSTWYNSLLTVICSALSLWLVQGIIVWATTKAQ---------------WAVIQV 50
           W+R+NLFS W+N++LT+  + L +  V  ++ W    A                W  I  
Sbjct: 19  WMRENLFSGWFNTVLTLGVAYLLVTSVGPLLNWFFLDANFVGSDPSACTGAGACWLFISQ 78

Query: 51  NLRLFLVGRFPQTEYWRVWIVLAIASTLGAVTAGIFFNQQKLTWRKVGLFAFIVGLLLIL 110
            L  F+ G +P    WRV ++                                       
Sbjct: 79  RLNFFIYGFYPDELQWRVDVMF-------------------------------------- 100

Query: 111 FTLDLSSRLWLLLTAVLLIPGFLLGSRLTNLVAPWLSLIWLLSFPIILWLI--GGGFGLR 168
                      LL AV  +P F+   R       WL L  +   PI+ + +  GG FGL 
Sbjct: 101 -----------LLLAVSFVPQFI--ERFPG--RKWLGLFGIFGLPIVGYFLIPGGSFGLE 145

Query: 169 PVSSNLWNGLLLTLLMAAISIVLSFPIGVLLALGRTSNLPVVRWFSILYIEIVRGVPLIG 228
            V S+ W GL+LTL++A I I+ S PIG+LLALGR S++P++R   +++IE+ R VPLI 
Sbjct: 146 EVQSSKWGGLMLTLILAYIGIIASLPIGILLALGRRSDMPIIRGICVVFIEVWRAVPLIT 205

Query: 229 ILFLAQVMLPLFFAADVRLDRVLRAIAGLVLFSAAYMAENVRGGLQAVSRGQVEAAKALG 288
           +LF+A VMLPLF    V  +++ RA+ G+ L+ +AYMAE +RGGLQA+ RGQ EAA ALG
Sbjct: 206 VLFMASVMLPLFLPEGVNFEKLARALIGITLWQSAYMAEVIRGGLQAIPRGQYEAADALG 265

Query: 289 LNTFFVVLLIVLPQALRAVIPALVGQFIGLFKDTSLLSLVGLVELTGIARSILAQPQFIG 348
           L  +  + L++LPQAL+ VIP +V  FI LFKDT+L+ ++GL ++ G  +S +  P +  
Sbjct: 266 LGYWRKMGLVILPQALKMVIPGIVNTFISLFKDTTLVLIIGLFDILGTVQSTVTDPAWQN 325

Query: 349 RYAEVYLFIGLIYWLFCYSMSLASRRLERQLN 380
              E Y+F+   +W+FC+ +S  S+ LER+L+
Sbjct: 326 VAIEGYVFVAFCFWVFCFGISRYSQNLERKLD 357


Lambda     K      H
   0.332    0.145    0.452 

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: 502
Number of extensions: 25
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: 381
Length of database: 362
Length adjustment: 30
Effective length of query: 351
Effective length of database: 332
Effective search space:   116532
Effective search space used:   116532
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (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